Here is a list of all class members with links to the classes they belong to:

- b -

• B : protocols::surface_docking::SurfaceParameters
• b : core::scoring::packstat::PointPair , protocols::sic_dock::Vec3
• b1() : core::scoring::FACTSResidueInfo
• b1_ : core::scoring::FACTSResidueInfo
• b1_b2_Ktheta() : protocols::branch_angle::BranchParam2
• b1_b2_Ktheta_ : protocols::branch_angle::BranchParam2
• b1_b2_theta0() : protocols::branch_angle::BranchParam2
• b1_b2_theta0_ : protocols::branch_angle::BranchParam2
• b1_bond_angle_A() : protocols::branch_angle::BranchCoef1
• b1_bond_angle_A_ : protocols::branch_angle::BranchCoef1
• b1_bond_angle_B() : protocols::branch_angle::BranchCoef1
• b1_bond_angle_B_ : protocols::branch_angle::BranchCoef1
• b1_bond_angle_C() : protocols::branch_angle::BranchCoef1
• b1_bond_angle_C_ : protocols::branch_angle::BranchCoef1
• b1_torsion_offset_A() : protocols::branch_angle::BranchCoef1
• b1_torsion_offset_A_ : protocols::branch_angle::BranchCoef1
• b1_torsion_offset_B() : protocols::branch_angle::BranchCoef1
• b1_torsion_offset_B_ : protocols::branch_angle::BranchCoef1
• b1_torsion_offset_C() : protocols::branch_angle::BranchCoef1
• b1_torsion_offset_C_ : protocols::branch_angle::BranchCoef1
• b2() : core::scoring::FACTSResidueInfo
• b2_ : core::scoring::FACTSResidueInfo
• b2_bond_angle_A() : protocols::branch_angle::BranchCoef2
• b2_bond_angle_A_ : protocols::branch_angle::BranchCoef2
• b2_bond_angle_B() : protocols::branch_angle::BranchCoef2
• b2_bond_angle_B_ : protocols::branch_angle::BranchCoef2
• b2_bond_angle_C() : protocols::branch_angle::BranchCoef2
• b2_bond_angle_C_ : protocols::branch_angle::BranchCoef2
• b2_torsion_offset_A() : protocols::branch_angle::BranchCoef2
• b2_torsion_offset_A_ : protocols::branch_angle::BranchCoef2
• b2_torsion_offset_B() : protocols::branch_angle::BranchCoef2
• b2_torsion_offset_B_ : protocols::branch_angle::BranchCoef2
• b2_torsion_offset_C() : protocols::branch_angle::BranchCoef2
• b2_torsion_offset_C_ : protocols::branch_angle::BranchCoef2
• B2I_1 : protocols::sparta::ANN
• B2I_2 : protocols::sparta::ANN
• B2I_3 : protocols::sparta::ANN
• B2L1_1 : protocols::sparta::ANN
• B2L1_2 : protocols::sparta::ANN
• B2L1_3 : protocols::sparta::ANN
• B2L2_1 : protocols::sparta::ANN
• B2L2_2 : protocols::sparta::ANN
• B2L2_3 : protocols::sparta::ANN
• B_ : core::scoring::constraints::KarplusFunc , protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• b_ : core::scoring::electron_density::KromerMann , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcs2::PcsTensor
• b_ang_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• b_evaluate_incoming_decoys_ : protocols::jd2::archive::EvaluatedArchive
• B_Factor : protocols::sparta::CORdata
• b_flag_is_present_ : core::chemical::Selector_CMDFLAG
• b_has_constraint_claimer : protocols::topology_broker::CmdLineData
• b_input_is_fullatom_ : protocols::abinitio::KinematicTaskControl
• b_len_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• b_return_unrelaxed_fullatom_ : protocols::abinitio::AbrelaxMover
• ba : protocols::loophash::LegacyLeapIndex
• bab_motif() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• bab_motifs() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• bab_motifs_ : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• backbone_ : protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::simple_filters::AtomicContactFilter
• backbone_backbone_acceptor_ : core::scoring::hbonds::HBondSet
• backbone_backbone_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• backbone_backbone_distance_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• backbone_backbone_donor_ : core::scoring::hbonds::HBondSet
• 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_backbone_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• backbone_burial() : core::scoring::rna::RNA_DataInfo
• backbone_burial_ : core::scoring::rna::RNA_DataInfo , protocols::rna::RNA_DataReader
• backbone_database() : protocols::loophash::LoopHashLibrary
• backbone_dihedral_scores_ : core::scoring::disulfides::NCaCaC_Dihedral_Func
• backbone_exposed() : core::scoring::rna::RNA_DataInfo
• backbone_exposed_ : core::scoring::rna::RNA_DataInfo , protocols::rna::RNA_DataReader
• backbone_for_moltenres_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_for_resid_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_index_map_ : protocols::loophash::LoopHashMap
• backbone_only() : protocols::match::upstream::BuildSet
• backbone_only_ : protocols::forge::remodel::RemodelEnzdesCstModule , protocols::match::upstream::BuildSet , protocols::swa::InputStreamWithResidueInfo
• 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_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
• background_energies_ : protocols::pack_daemon::PackDaemon
• background_node_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• background_node_index_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• BackgroundEdgeList : core::pack::interaction_graph::FirstClassNode< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• BackgroundEdgeListConstIter : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• BackgroundEdgeListIter : core::pack::interaction_graph::FirstClassNode< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• BackgroundEdgeVector : core::pack::interaction_graph::FirstClassNode< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G >
• BackgroundEdgeVectorIter : core::pack::interaction_graph::FirstClassNode< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G >
• BackgroundNode() : core::pack::interaction_graph::BackgroundNode< V, E, G >
• BackgroundNodeVector : core::pack::interaction_graph::FirstClassNode< V, E, G > , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• BackgroundToFirstClassEdge() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• BackgroundToFirstClassEdge< V, E, G > : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• backptr_ : core::sequence::Cell
• backrub() : protocols::dna::DesignProteinBackboneAroundDNA
• backrub_ : protocols::enzdes::EnzRepackMinimize , protocols::forge::remodel::RemodelMover::instruction_flags
• backrub_move() : protocols::flexpep_docking::FlexPepDockingProtocol
• backrub_mover_ : protocols::backrub::BackrubSidechainMover
• backrub_moves_ : protocols::protein_interface_design::movers::BackrubDDMover
• backrub_opt : protocols::flexpep_docking::FlexPepDockingFlags
• backrub_partner1_ : protocols::protein_interface_design::movers::BackrubDDMover
• backrub_partner2_ : protocols::protein_interface_design::movers::BackrubDDMover
• 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_deviation_ : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• backward_jump() : protocols::motifs::Motif
• backward_jump_ : protocols::motifs::Motif
• backward_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• backward_threshold_ : protocols::simple_moves::WobbleMover
• BAD : core::scoring::Energies
• bad : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage , protocols::jd2::InnerJob , protocols::jd2::Job
• bad_ : protocols::jd2::InnerJob
• bad_job_id_ : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• bad_jobs_ : protocols::jd2::MPIFileBufJobDistributor
• BAD_LOW_PROB : protocols::noesy_assign::CrossPeak
• bad_nter_ : protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::ModelCDRH3
• bad_tree() : core::kinematics::EXCN_InvalidFoldTree
• bad_tree_ : core::kinematics::EXCN_InvalidFoldTree
• bAlign_ : protocols::topology_broker::FibrilModelingClaimer
• Ball() : core::scoring::packing::Ball
• ball() : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• bAllowAdjacentJumps_ : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• balls() : core::scoring::packing::PoseBalls
• balls_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• band : core::scoring::sc::MolecularSurfaceCalculator
• BANGLE_MAX_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• BANGLE_MEAN_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• BANGLE_MIN() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• BANGLE_MIN_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• BANGLE_SD() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• BANGLE_SD_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• bAnnotate_ : core::fragment::FragmentIO
• bApplyEndBias_ : protocols::simple_moves::ClassicFragmentMover
• barcode_extend_stems() : protocols::LoopRebuild
• barea : core::scoring::packstat::LR_MP_AtomData
• barrier() : protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver
• Base : protocols::jd2::WriteFileSFB
• base() : protocols::dna::DNAParameters
• base2_xyz() : core::scoring::hbonds::hbtrie::HBAtom
• base2_xyz_ : core::scoring::hbonds::hbtrie::HBAtom
• BASE_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• base_ : core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , protocols::antibody::CDRH3Modeler
• base_atom_list_ : core::chemical::rna::RNA_ResidueType
• base_axis_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_axis_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_backbone_atom_dist_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_check_atom_neighbor_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_distance_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_rho_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_rho_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_table_size_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_z_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_z_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• base_base_only_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• base_centroid_screener_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• base_centroids() : core::scoring::rna::RNA_CentroidInfo
• base_centroids_ : core::scoring::rna::RNA_CentroidInfo
• base_geometry_height_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_geometry_height_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_geometry_orientation_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_geometry_orientation_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_ID_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• base_ID_old_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• base_name() : core::chemical::carbohydrates::CarbohydrateInfo , core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• base_only() : protocols::dna::RestrictDesignToProteinDNAInterface
• base_only_ : protocols::dna::DnaInterfaceFinder , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::RotamerDNAHBondFilter
• Base_pair() : core::scoring::rna::Base_pair
• base_pair_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_pair_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_pair_axis_cutoff_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_pair_dist_max_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_pair_dist_min_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_pair_planarity_cutoff_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_pair_rho_max_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_pair_rho_min_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_pair_score() : core::scoring::dna::DNA_BasePotential
• base_pair_z_offset_cutoff_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_pairing_count : protocols::swa::rna::SillyCountStruct
• base_pairing_only_screen_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• BASE_PARTNER : core::pose::datacache::CacheableDataType
• base_pseudo_atom_centers_ : core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::LK_hack
• base_pseudo_atom_f1_f2s_ : core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::LK_hack
• base_rep_score : protocols::swa::rna::FB_Pose_Data
• base_restype_name() : core::chemical::ResidueType
• base_restype_name_ : core::chemical::ResidueType
• base_score() : core::scoring::dna::DNA_BasePotential
• base_score_ : core::scoring::disulfides::Cb_Distance_Func
• Base_stack() : core::scoring::rna::Base_stack
• base_stack_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stack_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stack_axis_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stack_axis_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stack_axis_cutoff_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_stack_count : protocols::swa::rna::SillyCountStruct
• base_stack_dist_cutoff_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_stack_max_height_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_min_height_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_planarity_cutoff_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_stack_radius2_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_radius_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_rho_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_z_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_z_offset_max_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_stack_z_offset_min_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_stagger_array() : core::scoring::rna::RNA_RawBaseBaseInfo
• base_stagger_array_ : core::scoring::rna::RNA_RawBaseBaseInfo
• base_state_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• base_state_list_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• base_std_ID_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• base_std_ID_old_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• base_step_score() : core::scoring::dna::DNA_BasePotential
• base_string() : core::scoring::dna::DNA_BasePotential
• base_stub_list_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener
• base_stubs() : core::scoring::rna::RNA_CentroidInfo
• base_stubs_ : core::scoring::rna::RNA_CentroidInfo
• base_tag : protocols::swa::rna::FB_Pose_Data
• base_weight() : protocols::topology_broker::weights::ConstAbinitioMoverWeight
• base_xyz() : core::scoring::hbonds::hbtrie::HBAtom
• base_xyz_ : core::scoring::hbonds::hbtrie::HBAtom
• basebaseAtomIDs : protocols::motifs::Motif
• basebin_ : protocols::match::VoxelSetIterator
• BaseClass : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FragmentSampler , protocols::abinitio::Protocol
• BaseEtableEnergy() : core::scoring::etable::BaseEtableEnergy< Derived >
• basehalfbin_ : protocols::match::VoxelSetIterator
• BaseJobDistributor() : protocols::jobdist::BaseJobDistributor
• baseline() : protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter
• baseline_ : protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::Sigmoid
• baseline_checkpointing_filename() : protocols::simple_filters::Sigmoid
• baseline_checkpointing_filename_ : protocols::simple_filters::Sigmoid
• baseline_val() : protocols::simple_filters::RelativePoseFilter
• baseline_val_ : protocols::simple_filters::RelativePoseFilter
• basepair() : protocols::dna::DNAParameters
• basepair_axis_stagger_scaling() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• basepair_axis_stagger_scaling_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• basepair_xy_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• basepair_xy_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• basepair_xy_table_size_ : core::scoring::rna::RNA_LowResolutionPotential
• basepair_xy_z_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• basepairs_ : protocols::dna::DNAParameters
• 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
• baserots_offsets_ : core::pack::rotamer_set::ContinuousRotamerSet
• bases_ : protocols::dna::DNAParameters
• bases_begin() : protocols::dna::DNAParameters
• bases_end() : protocols::dna::DNAParameters
• basestack_axis_scaling() : core::scoring::rna::RNA_FilteredBaseBaseInfo
• basestack_axis_scaling_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• basestep() : protocols::dna::DNAParameters
• basesteps_ : protocols::dna::DNAParameters
• basesteps_begin() : protocols::dna::DNAParameters
• basesteps_end() : protocols::dna::DNAParameters
• BasicDataCache : core::conformation::RotamerSetBase , core::pose::Pose , core::scoring::Energies
• BasicDataCacheOP : core::conformation::RotamerSetBase , core::pose::Pose
• 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_features_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• batch_get_xyz() : core::conformation::Conformation , core::pose::Pose
• batch_id : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage
• batch_id_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB , protocols::jd2::archive::Batch
• batch_relax_ : protocols::hybridization::HybridizeProtocol
• batch_relax_absolute_max_ : protocols::loophash::MPI_LoopHashRefine_Master
• batch_relax_chunks_ : protocols::loophash::MPI_LoopHashRefine_Master
• batch_set_xyz() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::pose::Pose
• batch_size_ : protocols::loophash::LoopHashMoverWrapper
• batch_underflow() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor
• batches() : protocols::jd2::archive::ArchiveManager
• batches_ : protocols::jd2::archive::ArchiveManager , protocols::jd2::JobDistributor
• BatchFeatures() : protocols::features::BatchFeatures
• BatchFeaturesCreator() : protocols::features::BatchFeaturesCreator
• BatchJobInputter() : protocols::jd2::BatchJobInputter
• BatchList : protocols::abinitio::HedgeArchive , protocols::jd2::archive::ArchiveManager
• BatchNrEvaluator() : protocols::simple_filters::BatchNrEvaluator
• BatchStructuresMap : protocols::abinitio::HedgeArchive
• bb() : protocols::dna::DnaInterfaceMinMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::TaskAwareMinMover
• BB : protocols::topology_broker::DofClaim
• bb_ : protocols::dna::DnaInterfaceMinMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex , protocols::match::Bool3DGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::OccupiedSpaceHash , protocols::match::VoxelSetIterator , protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::RepGrid , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::TaskAwareMinMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes
• bb_acc_avail() : core::scoring::hbonds::HBondResidueMinData
• bb_acc_avail_ : core::scoring::hbonds::HBondResidueMinData
• bb_backrub_ : protocols::enzdes::EnzdesBaseProtocol
• bb_bb() : protocols::simple_filters::EnergyPerResidueFilter
• bb_bb_ : protocols::protein_interface_design::filters::HbondsToResidueFilter , 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_ : core::pack::interaction_graph::SimpleEdge
• bb_bbE_calced() : 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_bounding_sphere_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• bb_C_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_C_index_ : core::scoring::methods::ResidueCartBondedParameters
• bb_CA_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_CA_index_ : core::scoring::methods::ResidueCartBondedParameters
• bb_centroid() : core::pack::interaction_graph::SimpleNode
• bb_centroid_ : core::pack::interaction_graph::SimpleNode
• bb_clashes_ : protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• bb_clones() : core::conformation::symmetry::SymmetryInfo
• bb_clones_ : core::conformation::symmetry::SymmetryInfo
• bb_dihedral_tolerance_ : protocols::fldsgn::SheetConstraintsRCG
• bb_don_avail() : core::scoring::hbonds::HBondResidueMinData
• bb_don_avail_ : core::scoring::hbonds::HBondResidueMinData
• bb_donor_acceptor_check() : core::scoring::hbonds::HBondOptions
• bb_donor_acceptor_check_ : core::scoring::hbonds::HBondOptions
• bb_extended_ : protocols::match::Bool3DGrid
• bb_follows() : core::conformation::symmetry::SymmetryInfo
• bb_follows_ : core::conformation::symmetry::SymmetryInfo
• bb_fourier_data : core::scoring::dna::DNABFormPotential
• bb_grid_ : protocols::match::downstream::DownstreamBuilder , protocols::match::Matcher
• bb_H_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_H_index_ : core::scoring::methods::ResidueCartBondedParameters
• bb_hbond_ : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• bb_interface_builder_ : protocols::ligand_docking::MoveMapBuilder
• bb_interface_cutoff_ : protocols::ligand_docking::LigandBaseProtocol
• bb_is_independent() : core::conformation::symmetry::SymmetryInfo
• bb_min_ : protocols::enzdes::EnzdesBaseProtocol
• bb_min_allowed_dev_ : protocols::enzdes::EnzdesBaseProtocol
• bb_moves_ : protocols::enzdes::BackboneSampler
• bb_N_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_N_index_ : core::scoring::methods::ResidueCartBondedParameters
• bb_O_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_Pos : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::SS_Info2
• bb_pos_ : core::scoring::SS_Info , protocols::fldsgn::topology::SS_Info2
• bb_precision_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• bb_radius() : core::pack::interaction_graph::SimpleNode
• bb_radius_ : core::pack::interaction_graph::SimpleNode
• bb_sc_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• bb_stats() : core::scoring::orbitals::OrbitalsStatistics
• bbC_ : core::scoring::methods::ProClosureEnergy
• BBClaim() : protocols::topology_broker::BBClaim
• bbconf_for_rotamer() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• bbconf_for_rotamer_of_moltenres_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• bbconf_for_rotamer_on_moltenres() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• BBConRotMover() : protocols::simple_moves::BBConRotMover
• bbdb_ : protocols::loophash::LoopHashLibrary
• bbdb_range() : protocols::loophash::LoopHashMap
• bbdep_angle_parameters() : core::scoring::methods::ResidueCartBondedParameters
• bbdep_angle_params_ : core::scoring::methods::ResidueCartBondedParameters
• bbdep_bond_devs() : core::scoring::methods::IdealParametersDatabase
• bbdep_bond_devs_ : core::scoring::methods::IdealParametersDatabase
• bbdep_bond_params() : 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_length_params_ : core::scoring::methods::ResidueCartBondedParameters
• bbdep_nrc_interpdata_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_nrchi_binsize_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_nrchi_nbins_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_nrchi_sample() : core::pack::dunbrack::BBDepSemiRotamericData< T >
• bbdep_nrchi_sample_ : core::pack::dunbrack::BBDepSemiRotamericData< T >
• bbdep_nrchi_score() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_rotamers_to_sample_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbdep_rotsample_sorted_order_ : 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 >
• BBdisplay_state : protocols::viewer::GraphicsState
• bbdof_list : protocols::protein_interface_design::movers::ResidueBBDofs
• BBDofs() : protocols::protein_interface_design::movers::BBDofs
• bbdofs_ : protocols::protein_interface_design::movers::ResidueBBDofs
• BBG8T3AMover() : protocols::simple_moves::BBG8T3AMover
• bbg_move_prob_ : protocols::protein_interface_design::movers::BackrubDDMover
• BBGaussianMover() : protocols::simple_moves::BBGaussianMover
• bbgrid() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::upstream::UpstreamBuilder
• bbgrid_ : protocols::match::downstream::DownstreamAlgorithm , protocols::match::upstream::UpstreamBuilder
• bbgrid_set() : protocols::match::downstream::DownstreamBuilder
• bbind_chisamples_for_rotamer_chi() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_non_rotameric_chi_scores_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_binsize_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_nbins_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_sample() : core::pack::dunbrack::BBIndSemiRotamericData< T >
• bbind_nrchi_sample_ : core::pack::dunbrack::BBIndSemiRotamericData< T >
• bbind_nrchi_sampling_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_score() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_nrchi_scoring_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_rotamers_sorted_by_probability_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• bbind_rotamers_to_sample_ : 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 >
• bbl_ : protocols::scoring::ImplicitFastClashCheck
• bbl_ca_ : protocols::scoring::ImplicitFastClashCheck
• bbN_ : core::scoring::methods::ProClosureEnergy
• bbO_ : core::scoring::methods::ProClosureEnergy
• bbpos_is_set() : protocols::fldsgn::topology::SS_Info2
• bbpos_is_set_ : protocols::fldsgn::topology::SS_Info2
• BBrms : protocols::loophash::FilterBucket
• bbtorsion_srfd() : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• BBTorsionAndAnglesSRFD() : core::fragment::BBTorsionAndAnglesSRFD
• BBTorsionSRFD : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue , core::fragment::BBTorsionSRFD
• BBTorsionSRFDOP : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• bCentroid_ : protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• bcfl : core::scoring::APBSConfig::I_PARAM
• bChainbreaksAlwaysActive_ : protocols::abinitio::JumpingFoldConstraints
• bCmdFlag_ : protocols::topology_broker::ConstraintClaimer
• bCombineNoesyCst_ : protocols::abinitio::IterativeBase
• bCreateOutput_ : protocols::sparta::Sparta
• bCstAllAtom_ : protocols::abinitio::LoopJumpFoldCst
• bDoBetaJumping_ : protocols::abinitio::IterativeBase
• BDR() : protocols::forge::components::BDR
• BDRSegmentInfo() : protocols::forge::components::BDRSegmentInfo
• bdx : core::scoring::packstat::LR_MP_AtomData
• bdy : core::scoring::packstat::LR_MP_AtomData
• bead_bead_interaction : core::scoring::etable::AtomPairEnergy
• bead_names_ : core::coarse::Translator
• BeadAdder() : core::coarse::Rule::BeadAdder
• BeadAtom() : core::coarse::Translator::BeadAtom
• BeadList : core::coarse::Translator
• BeadName : core::coarse::Rule
• BeadNames : core::coarse::Translator
• BeadRules : core::coarse::Rule
• beads_ : core::coarse::Translator
• before_chain_break_grid_index_screening : protocols::swa::rna::SillyCountStruct
• before_minimization_reference_energies_ : protocols::optimize_weights::IterativeOptEDriver
• begin : core::fragment::picking_old::concepts::Extent< PageIterator > , protocols::forge::remodel::WorkingRemodelSet , 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
• begin1_ : core::scoring::dssp::StrandPairing , protocols::fldsgn::topology::StrandPairing
• begin2() : protocols::fldsgn::topology::StrandPairing
• begin2_ : core::scoring::dssp::StrandPairing , protocols::fldsgn::topology::StrandPairing
• begin_ : protocols::fldsgn::topology::SS_Base , protocols::jd2::parser::FragmentReader , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• 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
• behavior_ : core::pack::task::operation::AddBehaviorRLT
• behavior_non_catalytic_ : protocols::enzdes::SetCatalyticResPackBehavior
• behaviors_ : core::pack::task::ResidueLevelTask_
• 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
• being_packed_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• bEnableCcdMoves_ : protocols::loops::loop_closure::ccd::LoopClosure
• benchmark_ : protocols::antibody::AntibodyModeler , protocols::antibody::CDRH3Modeler , protocols::antibody::GraftMover , protocols::antibody::GraftOneMover , protocols::antibody::CloseOneMover , protocols::antibody::LoopRlxMover , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::CloseOneCDRLoop , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::GraftOneCDRLoop , protocols::antibody2::H3CterInsert , protocols::antibody2::H3RefineCCD , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::ModelCDRH3 , protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::RefineOneCDRLoopCentroid , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover
• bend() : protocols::fldsgn::topology::Helix
• bend_ : protocols::fldsgn::topology::Helix
• bend_angle_ : protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• bEnumeratedLastTime_ : protocols::abinitio::IterativeBase
• BesselI0() : core::scoring::CenHBPotential
• best_ : core::optimization::GA_Minimizer , protocols::simple_moves::sidechain_moves::SidechainMCMover
• best_abs_log_norm_ratio : core::optimization::symmetry::MinDebug , core::optimization::SimpleDerivCheckResult
• best_abs_log_norm_ratio_ : core::optimization::SimpleDerivCheckResult
• best_address_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• best_assignment() : protocols::pack_daemon::PackDaemon
• best_assignment_ : protocols::pack_daemon::PackDaemon
• best_assignment_valid_ : protocols::pack_daemon::PackDaemon
• best_by_ala_scan() : protocols::seeded_abinitio::SeedFoldTree
• best_candidate_rmsds_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• best_combine_score_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• best_cos_theta : core::optimization::symmetry::MinDebug , core::optimization::SimpleDerivCheckResult
• best_cos_theta_ : core::optimization::SimpleDerivCheckResult
• best_energy_ : protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::swa::RigidBodySampler
• best_entities() : protocols::genetic_algorithm::GeneticAlgorithm
• best_entity_ : protocols::pack_daemon::PackDaemon
• best_entity_positive_states_ : protocols::multistate_design::MultiStateFitnessFunction
• best_exemplar : protocols::cluster::DataPoint
• best_fitness_ : protocols::multistate_design::MultiStateFitnessFunction
• best_fitness_from_current_generation() : protocols::genetic_algorithm::GeneticAlgorithm
• best_fragment_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• best_Kmer_rms() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• best_match_dspos1s_ : protocols::match::output::BestMatchesCollection
• best_matches_ : protocols::match::output::BestMatchesCollection
• best_motifhits() : protocols::motifs::BuildPosition
• best_motifhits_ : protocols::motifs::BuildPosition
• best_motifs() : protocols::motifs::BuildPosition
• best_motifs_ : protocols::motifs::BuildPosition
• best_norm_analytic : core::optimization::symmetry::MinDebug , core::optimization::SimpleDerivCheckResult
• best_norm_analytic_ : core::optimization::SimpleDerivCheckResult
• best_norm_numeric : core::optimization::symmetry::MinDebug , core::optimization::SimpleDerivCheckResult
• best_norm_numeric_ : core::optimization::SimpleDerivCheckResult
• best_packscore_ : protocols::flxbb::FilterStructs_Packstat
• best_pose_ : protocols::flxbb::FilterStructs
• best_rot_bumpenergy_ : core::pack::rotamer_set::BumpSelector
• best_rotamer_energy() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::CoarseSingleResidueLibrary , core::pack::dunbrack::SingleResidueRotamerLibrary , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SingleLigandRotamerLibrary
• best_rotamers() : protocols::motifs::BuildPosition
• best_rotamers_ : protocols::motifs::BuildPosition
• best_score() : protocols::multistate_design::SingleState , protocols::relax::SRelaxPose
• best_score_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::multistate_design::SingleState
• best_score_log : protocols::relax::SRelaxPose
• best_struct : protocols::relax::SRelaxPose
• best_valid_ : core::optimization::Particle
• bestenergy() : core::pack::annealer::SimAnnealerBase
• bestenergy_ : core::pack::annealer::SimAnnealerBase
• BestHotspotCstMover() : protocols::protein_interface_design::movers::BestHotspotCstMover
• BestMatchesCollection() : protocols::match::output::BestMatchesCollection
• bestrotamer_at_seqpos() : core::pack::annealer::SimAnnealerBase
• bestrotamer_at_seqpos_ : core::pack::annealer::SimAnnealerBase
• BestTotalScoreSelector() : protocols::frag_picker::BestTotalScoreSelector
• beta() : core::scoring::CSA , Transformation , protocols::protein_interface_design::Transformation , protocols::swa::rna::Euler_angles , core::pose::Pose , protocols::dna::DNABase
• beta_ : protocols::dna::DNABase , core::scoring::CSA , protocols::simple_filters::AbinitioBaseFilter , protocols::swa::RigidBodySampler
• BETA_A_FORM : protocols::rna::RNA_HelixAssembler
• beta_atom_names_ : core::scoring::dna::DNATorsionPotential
• beta_barrel_ : core::scoring::MembraneTopology
• beta_bins_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• beta_components() : core::scoring::dna::DNATorsionPotential
• beta_components_ : core::scoring::dna::DNATorsionPotential
• beta_potential_ : core::scoring::rna::RNA_TorsionPotential
• beta_ratio_ : protocols::simple_filters::AbinitioBaseFilter
• beta_turn_distance_cutoff : protocols::features::BetaTurnDetectionFeatures
• beta_turn_length : protocols::features::BetaTurnDetectionFeatures
• 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
• bExclusive_ : protocols::topology_broker::RigidChunkClaimer
• bF() : protocols::frag_picker::VallResidue
• bF_ : protocols::frag_picker::VallResidue
• bfac : core::scoring::packstat::SimplePDB_Atom , core::scoring::packing::PoseBalls
• bfac_ : core::scoring::packing::PoseBalls
• BFactor() : protocols::frag_picker::scores::BFactor
• BfactorMPM() : protocols::match::BfactorMPM
• bForceSingleSheet_ : protocols::jumping::SheetBuilder
• bFullatom_ : protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• bg_bg_atom_atom_overlaps_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_bg_respairs_w_hphobe_olap_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_edge_list_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• bg_edge_vector_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• bg_edge_vector_up_to_date_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• bg_exp_hphobe_djs_offsets_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_mean_ : core::scoring::constraints::MixtureFunc
• bg_n_exp_hphobes_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_neighbor_map : core::pack::interaction_graph::SurfaceNode< V, E, G >
• bg_node_2_resid() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• bg_node_vector_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• bg_nodes_ : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• bg_nodes_near_rotsub_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_nodes_near_rotsub_bool_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• bg_res_num_atoms_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• bg_residues_ : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• bg_sd_ : core::scoring::constraints::MixtureFunc
• bg_to_fc_edge_list_ : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• bGDT_ : protocols::simple_filters::RmsdEvaluator
• bgenumeration_2_resid_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• Bi() : core::scoring::FACTSResidueInfo
• Bi_ : core::scoring::FACTSResidueInfo
• BI_1 : protocols::sparta::ANN
• BI_2 : protocols::sparta::ANN
• BI_3 : protocols::sparta::ANN
• BiasedFragmentMover() : protocols::nonlocal::BiasedFragmentMover
• bIdealLoopClosing() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• bIdealLoopClosing_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• big_ : protocols::seeded_abinitio::SegmentHybridizer
• big_angle_ : protocols::simple_moves::BackboneMover
• BIG_BULGE_LIMIT : core::scoring::dssp::StrandPairing
• big_frag_insertion_weight_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::FoldTreeHybridize
• BigBinConstraint() : core::scoring::constraints::BigBinConstraint
• BigBinConstraintCreator() : core::scoring::constraints::BigBinConstraintCreator
• bIgnoreSequenceSeparation() : protocols::abinitio::FoldConstraints
• bIgnoreSequenceSeparation_ : protocols::abinitio::FoldConstraints
• BIN : protocols::sic_dock::SICFast
• bin() : core::scoring::constraints::BigBinConstraint
• Bin3D : protocols::match::Bool3DGrid , protocols::match::BumpGrid , protocols::match::Bool3DGridKinemageWriter
• Bin6D : protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::VoxelSetIterator
• bin_ : core::scoring::constraints::BigBinConstraint
• bin_angle() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• bin_center() : protocols::match::Bool3DGrid
• bin_dist_ : core::scoring::mm::MMLJEnergyTable
• 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_max_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• bin_min_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• bin_names_ : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• bin_offset_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• bin_probs_ : protocols::frag_picker::quota::ABEGO_SS_Config
• bin_rotameric_chi() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• bin_size_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer , protocols::frag_picker::scores::AdaptiveScoreHistogram , core::scoring::constraints::SplineFunc , protocols::scoring::methods::saxs::PDDFEnergy , protocols::swa::rna::RNA_LoopCloseSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper
• bin_width() : protocols::match::Bool3DGrid
• bin_width_ : core::scoring::carbon_hbonds::CarbonHBondPotential , protocols::match::Bool3DGrid , protocols::match::downstream::ActiveSiteGrid
• bin_width_2x_ : protocols::match::Bool3DGrid
• binary_ : protocols::outputter::SilentFileOutputter
• 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_rna_output_ : protocols::rna::RNA_DeNovoProtocol
• BinaryProteinSilentStruct() : core::io::silent::BinaryProteinSilentStruct
• BinaryProteinSilentStructCreator() : core::io::silent::BinaryProteinSilentStructCreator
• BinaryRNASilentStruct() : core::io::silent::BinaryRNASilentStruct
• BinaryRNASilentStructCreator() : core::io::silent::BinaryRNASilentStructCreator
• binding_E_ : protocols::dna::DnaInterfacePacker
• BindingSiteConstraint() : protocols::constraints_additional::BindingSiteConstraint
• BindingSiteConstraintCreator() : protocols::constraints_additional::BindingSiteConstraintCreator
• BindingStrainFilter() : protocols::protein_interface_design::filters::BindingStrainFilter
• bInit_ : protocols::abinitio::hConvergenceCheck , protocols::hybridization::hConvergenceCheck
• bInitDofs_ : protocols::topology_broker::FragmentClaimer
• binner() : protocols::match::HitHasher
• binner_ : protocols::match::HitNeighborFinder , protocols::match::MatchCounter
• bins1_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• bins2_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• bins3_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• bins_per_A2 : core::scoring::etable::Etable , core::scoring::etable::EtableOptions , core::scoring::etable::MembEtable
• bins_per_angstrom_squared_ : core::scoring::mm::MMLJEnergyTable
• bins_vect_ : core::scoring::constraints::SplineFunc
• bins_vect_size_ : core::scoring::constraints::SplineFunc
• binw_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• binwidth_dist : core::scoring::sc::MolecularSurfaceCalculator
• binwidth_norm : core::scoring::sc::MolecularSurfaceCalculator
• BIOPConstIterator : protocols::forge::components::VarLengthBuild , protocols::forge::build::BuildManager
• BIOPIterator : protocols::forge::build::BuildManager
• bitmask_for_position() : protocols::match::OccupiedSpaceHash
• bJumpFragMoves_ : protocols::abinitio::JumpingFoldConstraints
• bJumps_use_IntraResStub_ : core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• bKeepFilesAlive_ : protocols::jd2::MpiFileBuffer
• bKeepFragments_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• bKeepJumpsFromInputPose_ : protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::JumpClaimer
• bKeepStubInResidue_ : core::kinematics::Edge
• BL1_1 : protocols::sparta::ANN
• BL1_2 : protocols::sparta::ANN
• BL1_3 : protocols::sparta::ANN
• BL2_1 : protocols::sparta::ANN
• BL2_2 : protocols::sparta::ANN
• BL2_3 : protocols::sparta::ANN
• blacklist_ : protocols::wum::WorkUnitBase
• blanket_assign_state_0() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DensePDInteractionGraph , 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::PDInteractionGraph , 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 >
• bLocal_ : protocols::topology_broker::CoordConstraintClaimer
• block() : protocols::jd2::WriteFileSFB , protocols::jd2::SingleFileBuffer
• block_file() : protocols::jd2::MpiFileBuffer
• block_signals() : core::conformation::Conformation
• block_size() : core::graph::ArrayPool< T >
• block_size_ : core::graph::ArrayPool< T >
• blocked_files_ : protocols::jd2::MpiFileBuffer
• blocking_signals() : core::conformation::Conformation
• BLOSUM_62 : protocols::sparta::Sparta::SpartaLib
• blosum_matrix_ : protocols::frag_picker::scores::ProfileScoreBlosum62
• BluePrint : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::jd2::parser::BluePrint
• blueprint : protocols::forge::remodel::RemodelData
• BluePrint : protocols::fldsgn::BluePrintBDR , protocols::jd2::parser::BluePrint , protocols::flxbb::FlxbbDesign , protocols::jd2::parser::BluePrint
• blueprint_ : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintsRCG , protocols::forge::remodel::RemodelMover , protocols::jd2::parser::FragmentReader , protocols::flxbb::FlxbbDesign
• blueprint_cst_definition() : protocols::forge::remodel::RemodelEnzdesCstModule
• BluePrintBDR() : protocols::fldsgn::BluePrintBDR
• BluePrintOP : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintsRCG , protocols::fldsgn::BluePrintBDR , protocols::flxbb::FlxbbDesign
• bMinTrial_ : protocols::abinitio::FoldConstraints , protocols::abinitio::ConstraintFragmentSampler
• bNoRecoverLowAtSwitch_ : protocols::abinitio::ConstraintFragmentSampler
• BOGUS_ASSIGNMENTS : protocols::noesy_assign::PeakAssignmentResidueMap
• BOGUS_BATCH_ID : protocols::jd2::BatchJobInputter
• Boinc() : protocols::boinc::Boinc
• boinc_mode_ : protocols::canonical_sampling::CanonicalSamplingMover
• BoincCurrentPoseObserver() : protocols::boinc::BoincCurrentPoseObserver
• BOINCJobDistributor() : protocols::jd2::BOINCJobDistributor
• boltz_rank_ : protocols::simple_moves::GenericMonteCarloMover
• boltz_temp_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• boltzmann() : protocols::moves::MonteCarlo , protocols::simple_moves::TorsionDOFMover , protocols::moves::MonteCarlo , protocols::moves::ReplicaExchangeMC , protocols::simple_moves::GenericMonteCarloMover
• 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_central_atoms_to_score_ : core::scoring::methods::EnergyMethodOptions
• bond_angle_dof_id() : core::kinematics::AtomTree
• bond_angle_map_ : protocols::backrub::BackrubMover
• bond_angle_residue_type_param_set() : core::scoring::methods::EnergyMethodOptions , protocols::branch_angle::BranchAngleOptimizer , core::scoring::methods::EnergyMethodOptions , protocols::branch_angle::BranchAngleOptimizer
• bond_angle_residue_type_param_set_ : core::scoring::methods::EnergyMethodOptions , protocols::branch_angle::BranchAngleOptimizer
• bond_length() : core::kinematics::AtomTree , protocols::simple_moves::CutChainMover , core::conformation::Conformation
• bond_length_ : protocols::simple_moves::CutChainMover
• bond_length_dof_id() : core::kinematics::AtomTree
• bond_lengths_ : core::chemical::IdealBondLengthSet
• bond_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
• bond_type_data_set_ : core::chemical::sdf::CtabBase
• bondangle() : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• bondangle_atom_sets_ : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• bondangle_index() : core::scoring::mm::MMBondAngleResidueTypeParam
• bondangle_index_ : core::scoring::mm::MMBondAngleResidueTypeParam
• BondAngleKey : protocols::backrub::BackrubSegment
• bondangles_bbdep_def_ : core::scoring::methods::IdealParametersDatabase
• bondangles_bbdep_gly_ : core::scoring::methods::IdealParametersDatabase
• bondangles_bbdep_prepro_ : core::scoring::methods::IdealParametersDatabase
• bondangles_bbdep_pro_ : core::scoring::methods::IdealParametersDatabase
• bondangles_bbdep_valile_ : core::scoring::methods::IdealParametersDatabase
• bondangles_for_atom() : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• bondangles_for_atom_ : core::chemical::ResidueType , core::scoring::mm::MMBondAngleResidueTypeParam
• bondangles_indep_ : core::scoring::methods::IdealParametersDatabase
• BondData() : core::chemical::sdf::BondData
• bonded() : core::chemical::AutomorphismIterator
• bonded_atom_name : core::chemical::sdf::addedH
• bonded_neighbor() : core::chemical::ResidueType , core::conformation::Residue
• bonded_neighbor_ : core::chemical::ResidueType
• bonded_neighbor_all_res() : core::conformation::Conformation
• bonded_neighbor_type_ : core::chemical::ResidueType
• bonded_neighbor_types() : core::chemical::ResidueType
• bonded_orbitals() : core::chemical::ResidueType , core::conformation::Residue
• BondedAtom() : core::kinematics::tree::BondedAtom
• BondID() : core::id::BondID
• bondlen_precision_ : protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jd2::AtomTreeDiffJobOutputter
• bondlengths_bbdep_def_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_bbdep_gly_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_bbdep_prepro_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_bbdep_pro_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_bbdep_valile_ : core::scoring::methods::IdealParametersDatabase
• bondlengths_indep_ : core::scoring::methods::IdealParametersDatabase
• bondlist : protocols::cartesian::MolecularDynamics
• bonds_scorefxn_ : protocols::hybridization::CartesianHybridize , protocols::seeded_abinitio::SegmentHybridizer
• bondType : core::chemical::sdf::BondData
• bonus_ : core::scoring::constraints::ResidueTypeLinkingConstraint , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , core::pack::dunbrack::DunbrackConstraint
• bonus_value() : protocols::hotspot_hashing::HotspotStub
• bonus_value_ : protocols::hotspot_hashing::HotspotStub
• Book() : core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::concepts::Library< Books > , core::fragment::picking_old::vall::VallSections
• BookConstIterator : core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::concepts::Library< Books > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• BookIterator : core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::concepts::Library< Books > , core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• BookmarkConstIterator : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• BookmarkIterator : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• Bookmarks : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallLibrarian
• bookmarks() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• bookmarks_ : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• books() : core::fragment::picking_old::concepts::Library< Books >
• 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_cycles_ : protocols::forge::remodel::RemodelLoopMover
• boost_closure_stage() : protocols::forge::remodel::RemodelLoopMover
• boost_fa_atr : protocols::flexpep_docking::FlexPepDockingFlags
• bootstrap_ : protocols::rbsegment_relax::RBSegmentRelax
• bootstrapCATrace() : protocols::rbsegment_relax::FragInsertAndAlignMover
• born_radius() : core::scoring::GenBornResidueInfo
• born_radius_ : core::scoring::GenBornResidueInfo
• both_count : protocols::swa::rna::SillyCountStruct
• both_criteria_needed_to_pass_ : protocols::match::NumNeighborsMPM
• BOTH_SC_AND_BB : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• bottom() : protocols::dna::DnaPosition
• bottom_ : protocols::dna::DnaPosition
• bound() : protocols::simple_filters::NonSequentialNeighborsFilter
• bound_ : protocols::simple_filters::NonSequentialNeighborsFilter , protocols::optimize_weights::DGBindOptEData , protocols::toolbox::task_operations::ProteinCore
• bound_energies_ : protocols::simple_moves::ddG
• bound_per_residue_energies_ : protocols::simple_moves::ddG
• bound_struct() : protocols::optimize_weights::DGBindOptEData
• bound_total_energy_ : protocols::simple_moves::ddG
• bound_width_ : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• boundary_ : protocols::toolbox::task_operations::SelectBySASAOperation
• 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
• BoundedCollectorCOP : protocols::frag_picker::BoundedCollector< StrictWeakOrdering >
• BoundedCollectorOP : protocols::frag_picker::BoundedCollector< StrictWeakOrdering >
• 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
• bounding_volumes_for_bb_for_aa_ : protocols::flexpack::interaction_graph::OTFFlexbbNode
• BoundingBox : protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::HitHasher , protocols::match::VoxelSetIterator , protocols::match::MatcherTask , protocols::match::OccupiedSpaceHash , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::Bool3DGrid , protocols::match::Matcher
• BoundingSphere : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• bounds_check() : core::graph::Array0< T >
• bounds_check_entity() : protocols::pack_daemon::EntityCorrespondence
• bounds_check_residue() : protocols::pack_daemon::EntityCorrespondence
• bOverlapChainbreaks_ : protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::ConstraintFragmentSampler
• box_size : protocols::ligand_docking::Transform_info
• bp_motifhits() : protocols::motifs::MotifSearch
• bp_rotamers() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• BP_type : core::scoring::dna::DNA_BasePotential
• bpdata_ : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• bpdata_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• bQuickTest() : protocols::abinitio::FragmentSampler , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• bQuickTest_ : protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• BR() : core::scoring::FACTSResidueInfo
• BR_ : core::scoring::FACTSResidueInfo
• bRama_check() : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• bRama_check_ : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• bRampChainbreak_ : protocols::loops::loop_closure::ccd::LoopClosure
• bRampChainbreaks_ : protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::ConstraintFragmentSampler
• bRampCoordConstraints_ : protocols::abinitio::ConstraintFragmentSampler
• branch_point() : core::chemical::carbohydrates::CarbohydrateInfo
• branch_point_atoms_ : core::chemical::ResidueType
• branch_points_ : core::chemical::carbohydrates::CarbohydrateInfo
• BranchAngleOptimizer() : protocols::branch_angle::BranchAngleOptimizer
• BranchCoef1() : protocols::branch_angle::BranchCoef1
• BranchCoef2() : protocols::branch_angle::BranchCoef2
• branchopt() : protocols::backrub::BackrubMover
• branchopt_ : protocols::backrub::BackrubMover
• BranchParam1() : protocols::branch_angle::BranchParam1
• BranchParam2() : protocols::branch_angle::BranchParam2
• bRandomSheet_ : protocols::topology_broker::TemplateJumpClaimer
• bRegenerateFromInputPose_ : protocols::topology_broker::CoordConstraintClaimer
• bRelax_ : protocols::abinitio::AbrelaxApplication
• BRENT() : core::optimization::BrentLineMinimization
• brent_abs_tolerance() : core::optimization::MinimizerOptions
• brent_abs_tolerance_ : core::optimization::MinimizerOptions
• BrentLineMinimization() : core::optimization::BrentLineMinimization
• Bridge() : protocols::forge::build::Bridge
• BRIDGE_RES_ : protocols::swa::StepWisePoseSetup
• bridge_res_ : protocols::swa::StepWisePoseSetup
• bRigidInRelax_ : protocols::topology_broker::RigidChunkClaimer
• 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_ : protocols::topology_broker::TopologyClaimer
• broker_file() : protocols::jd2::archive::Batch
• broking() : protocols::topology_broker::TopologyBroker
• brub_max_atoms_ : protocols::enzdes::EnzdesFlexBBProtocol
• brub_min_atoms_ : protocols::enzdes::EnzdesFlexBBProtocol
• brub_mover_ : protocols::enzdes::EnzdesFlexBBProtocol
• brub_pivot_atoms_ : protocols::enzdes::EnzdesFlexBBProtocol
• brute_move_large() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• brute_move_large_ : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio
• brute_move_small() : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio
• brute_move_small_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• brute_move_small_top25() : protocols::abinitio::MembraneAbinitio
• brute_move_small_top25_ : protocols::abinitio::MembraneAbinitio
• BruteFunGroupTK() : protocols::kinmatch::BruteFunGroupTK
• BS_type : core::scoring::dna::DNA_BasePotential
• bSampleJumps_ : protocols::abinitio::JumpingFoldConstraints
• bSkipOnNoViolation_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• bSkipStage1_ : protocols::abinitio::ClassicAbinitio
• bSkipStage2_ : protocols::abinitio::ClassicAbinitio
• bSkipStage3_ : protocols::abinitio::ClassicAbinitio
• bSkipStage4_ : protocols::abinitio::ClassicAbinitio
• bSkipStage5_ : protocols::abinitio::ClassicAbinitio
• bSlaveCanOpenFile_ : protocols::jd2::MpiFileBuffer
• bStealJumps_ : protocols::abinitio::JumpingFoldConstraints
• bStop_ : protocols::jd2::MpiFileBuffer
• bSuperimpose_ : protocols::topology_broker::CoordConstraintClaimer
• bucket_counts : core::scoring::electron_density::ElectronDensity
• bucket_id : core::scoring::electron_density::ElectronDensity
• buckle() : protocols::dna::DNABasepair
• buckle_ : protocols::dna::DNABasepair
• buf : protocols::sparta::Sparta::SpartaLib , protocols::sparta::ANN , protocols::sparta::GDB
• buf_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , core::io::serialization::BUFFER
• buf_to_address() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• BUFFER() : core::io::serialization::BUFFER
• buffer_factor_ : protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::quota::ABEGO_SS_Pool
• buffer_length_ : protocols::simple_moves::WobbleMover
• buffer_rank_ : protocols::jd2::MpiFileBuffer
• buffer_signals() : core::conformation::Conformation
• buffering_signals() : core::conformation::Conformation
• BufferMap : protocols::jd2::SingleFileBuffer
• Buffers : protocols::jd2::MpiFileBuffer
• build() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , core::chemical::AtomICoor , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::upstream::ProteinUpstreamBuilder , core::chemical::orbitals::ICoorOrbitalData , protocols::match::output::WriteUpstreamCoordinateKinemage , core::scoring::methods::WaterBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::ligand_docking::MoveMapBuilder , core::chemical::AtomICoor , protocols::match::downstream::DownstreamBuilder , protocols::ligand_docking::InterfaceBuilder , core::chemical::AtomICoor , protocols::match::upstream::UpstreamBuilder , protocols::match::downstream::DownstreamAlgorithm
• build_all_loops_ : protocols::loops::loop_mover::IndependentLoopMover
• build_atom_ideal() : core::conformation::Residue
• build_attempts_ : protocols::loops::loop_mover::IndependentLoopMover
• build_bbdep_rotamers() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• build_bbind_rotamers() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >
• build_centroid_loop() : protocols::antibody2::H3PerturbCCD , protocols::antibody::CDRH3Modeler
• build_conformer_group() : protocols::match::downstream::LigandConformerBuilder
• build_constraints() : protocols::abinitio::StrandConstraints , protocols::abinitio::AlternativePairings
• build_coords_for_clash_checking_ : protocols::match::downstream::TargetRotamerCoords
• build_cst_conformer_jumps() : protocols::jumping::ResiduePairJump
• build_dependent_rotamers() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSet_ , 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_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::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• build_inverted_rotamers() : protocols::motifs::Motif
• build_jumpres_distmap() : core::kinematics::ShortestPathInFoldTree
• build_loop_with_ccd_closure() : protocols::LoopRebuild
• build_loops() : 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::GenBornPotential , core::scoring::FACTSPotential
• build_point() : protocols::match::Matcher
• build_pose_from_scratch_ : protocols::swa::rna::StepWiseRNA_ResidueSampler
• build_positionOPs() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• build_positionOPs_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• build_query_loops_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• build_random_loops() : protocols::LoopRebuild
• build_residue_vector_from_fragment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• build_rotamer() : protocols::motifs::MotifHit
• build_rotamer_ : protocols::motifs::MotifHit
• build_rotamer_list() : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• build_rotamers() : protocols::flexpack::rotamer_set::FlexbbRotamerSets , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::ContinuousRotamerSet , protocols::motifs::Motif , core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSets
• 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_set_id_for_restype_ : protocols::match::Matcher
• build_sets_ : 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
• buildDisulfide : protocols::forge::remodel::WorkingRemodelSet
• builder_loop() : protocols::jumping::SheetBuilder
• BuildInstruction() : protocols::forge::build::BuildInstruction
• BuildInstructionCAPs : protocols::forge::build::BuildInstruction
• BuildInstructionOP : protocols::forge::remodel::RemodelMover , protocols::forge::components::BDR , protocols::fldsgn::BluePrintBDR
• BuildInstructionOPs : protocols::forge::build::BuildManager
• BuildManager : protocols::fldsgn::BluePrintBDR , protocols::forge::build::BuildManager , protocols::forge::components::BDR , protocols::forge::build::BuildManager , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover
• BuildPosition() : protocols::motifs::BuildPosition
• BuildPosition_from_Size() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• BuildSet() : protocols::match::upstream::BuildSet
• buildtype() : protocols::jd2::parser::BluePrint
• buildtype_ : protocols::jd2::parser::BluePrint
• bulge_at_chain_closure_count : protocols::swa::rna::SillyCountStruct
• bulge_res : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• bulge_res_ : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::StepWisePoseSetup
• bulge_res_base_state : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• bulge_res_pucker_state : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• bulge_suite : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• bump_check() : core::pack::task::PackerTask , protocols::flexpack::rotamer_set::FlexbbRotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::task::PackerTask_
• bump_check_ : core::pack::task::PackerTask_ , protocols::motifs::MotifSearch
• bump_check_backbone() : core::scoring::ScoreFunction
• bump_check_full() : core::scoring::ScoreFunction
• bump_cutoff_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover
• bump_energy_backbone() : core::scoring::methods::TwoBodyEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::ProClosureEnergy , core::scoring::etable::BaseEtableEnergy< Derived >
• bump_energy_full() : core::scoring::methods::ProClosureEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::MMLJEnergyInter , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::TwoBodyEnergy
• bump_grid() : protocols::match::output::MatchCollisionFilter
• bump_grid_ : protocols::match::output::MatchCollisionFilter
• bump_overlap_factor_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• bump_parameter() : core::scoring::rna::RNA_AtomVDW
• bump_selector_ : protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , core::pack::rotamer_set::RotamerSet_
• bump_threshold_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• BumpGrid() : protocols::match::BumpGrid
• BumpSelector() : core::pack::rotamer_set::BumpSelector
• bundle_size_ : protocols::features::helixAssembly::HelixBundleFeatures
• bur_dist_ : protocols::pockets::PocketGrid
• bur_score_ : protocols::pockets::PocketGrid
• burial_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• burial_function_ : core::scoring::rna::RNA_DataBackboneEnergy
• burial_sasa_cutoff_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• BurialEnergy() : core::scoring::methods::BurialEnergy
• buried : core::scoring::sc::Atom , core::scoring::sc::_DOT
• buried_area : core::scoring::packstat::AreaAccumulator
• BURIED_RESIDUE_NO_HSASA_CUTOFF : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfacePotential , core::pack::interaction_graph::SurfaceNode< V, E, G >
• BuriedPolarScore() : protocols::sic_dock::BuriedPolarScore
• BuriedUnsatHbondFilter() : protocols::simple_filters::BuriedUnsatHbondFilter
• BuriedUnsatisfiedPolars_ : protocols::analysis::InterfaceAnalyzerMover
• BuriedUnsatisfiedPolarsCalculator() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• bUseInputPose_ : protocols::topology_broker::StartStructClaimer , protocols::topology_broker::RigidChunkClaimer
• bUseJobPose_ : protocols::topology_broker::TopologyBroker
• bUseThreadingJobLoops_ : protocols::topology_broker::RigidChunkClaimer::JumpCalculator , protocols::topology_broker::RigidChunkClaimer
• bUseXYZ_in_cstfile_ : protocols::topology_broker::CoordConstraintClaimer
• bValidTree_ : protocols::jumping::JumpSample
• bWriteIntermediateFiles_ : protocols::jd2::SilentFileJobOutputter
• bWriteIntermediateStructures_ : protocols::jd2::SilentFileJobOutputter
• bWriteNoStructures_ : protocols::jd2::SilentFileJobOutputter
• bX_ : core::grid::CartGrid< T >
• bx_init() : core::optimization::MinimizerOptions
• bx_init_ : core::optimization::MinimizerOptions
• bY_ : core::grid::CartGrid< T >
• by_resid_ : protocols::noesy_assign::ResonanceList
• byte_index_from_doublebin() : protocols::match::Bool3DGrid
• bytes_ : protocols::moves::UDPSocketClient::UUID
• bZ_ : core::grid::CartGrid< T >