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

- b -

• B() : core::io::CrystInfo , core::scoring::electron_density::OneGaussianScattering
• b : core::scoring::packstat::PointPair
• B() : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::ligand_docking::ga_ligand_dock::hbAcc
• b : protocols::md::Constraint , protocols::pockets::UnionEdge , protocols::sic_dock::Vec3
• b1() : core::scoring::FACTSRsdTypeInfo
• b1_ : core::scoring::FACTSRsdTypeInfo
• 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::FACTSRsdTypeInfo
• b2_ : core::scoring::FACTSRsdTypeInfo
• 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::io::CrystInfo
• b_ : core::scoring::carbohydrates::CHIEnergyFunction , core::scoring::carbohydrates::OmegaPreferencesFunction , core::scoring::electron_density::KromerMann
• B_ : core::scoring::electron_density::poseCoord
• b_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::fiber_diffraction::KromerMann
• B_ : core::scoring::func::KarplusFunc
• b_ : core::scoring::ProQPotential , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• B_ : protocols::electron_density::DockIntoDensityMover , protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• b_ : protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• B_0 : protocols::ligand_docking::ga_ligand_dock::hbAcc
• b_allow_independent_alignment_per_fragment : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• b_ang_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• b_axis_ : protocols::docking::EllipsoidalRandomizationMover
• b_discard_lonely_SS_ : protocols::protein_interface_design::filters::SSamountFilter
• B_EPS : protocols::electron_density::BfactorMultifunc
• b_evaluate_incoming_decoys_ : protocols::jd2::archive::EvaluatedArchive
• B_Factor : protocols::sparta::PDB_Entry
• b_flag_is_present_ : core::chemical::Selector_CMDFLAG
• b_full_motif_bb_alignment : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• b_graft_only_hotspots_by_sidechain_replacement : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• b_has_constraint_claimer : protocols::topology_broker::CmdLineData
• b_input_is_fullatom_ : protocols::abinitio::KinematicTaskControl
• b_is_full_motif_bb_alignment() : protocols::motif_grafting::movers::MotifMatch
• b_len_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• b_max_ : protocols::cryst::FitBfactorsMover
• b_min_ : protocols::cryst::FitBfactorsMover
• b_proq2_ : core::scoring::ProQPotential
• b_return_unrelaxed_fullatom_ : protocols::abinitio::AbrelaxMover
• b_sharpen_ : protocols::electron_density::ScaleMapIntensities
• b_target_chain_ : protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SSamountFilter
• ba : protocols::denovo_design::components::IdealAbegoGenerator , protocols::loophash::LegacyLeapIndex
• ba_no_extension : protocols::denovo_design::components::IdealAbegoGenerator
• bab_motif() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• bab_motifs() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• bab_motifs_ : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• back() : protocols::jd2::JobsContainer
• backbone() : protocols::protein_interface_design::filters::HbondsToResidueFilter
• backbone1_2_target_ : core::scoring::constraints::BackboneStubConstraint
• backbone1_target_ : core::scoring::constraints::BackboneStubConstraint
• backbone2_target_ : core::scoring::constraints::BackboneStubConstraint
• backbone_ : protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::simple_filters::AtomicContactFilter
• backbone_aa() : core::chemical::ResidueTypeBase , core::conformation::Residue
• backbone_aa_ : core::chemical::ResidueTypeBase
• backbone_aa_raw() : core::chemical::ResidueTypeBase
• backbone_atom1_id_ : core::scoring::constraints::BackboneStubConstraint
• backbone_atom2_id_ : core::scoring::constraints::BackboneStubConstraint
• backbone_backbone() : protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideInternalHbondsMetric
• backbone_backbone_ : protocols::cyclic_peptide::PeptideInternalHbondsMetric
• 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::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_backbone_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• backbone_burial() : core::pose::rna::RNA_DataInfo
• backbone_burial_ : core::pose::rna::RNA_DataInfo
• backbone_burial_res_ : core::io::rna::RNA_DataReader
• backbone_database() : protocols::loophash::LoopHashLibrary
• backbone_dihedral_scores_ : core::scoring::disulfides::NCaCaC_Dihedral_Func
• backbone_exposed() : core::pose::rna::RNA_DataInfo
• backbone_exposed_ : core::pose::rna::RNA_DataInfo
• backbone_exposed_res_ : core::io::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_mover_ : protocols::coupled_moves::CoupledMovesProtocol , protocols::simple_moves::CoupledMover
• backbone_mover_complex_type_namer() : protocols::simple_moves::BackboneMover
• backbone_only() : protocols::match::upstream::BuildSet
• backbone_only_ : protocols::forge::remodel::RemodelEnzdesCstModule , protocols::match::upstream::BuildSet , protocols::simple_moves::CopyDofMover , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• backbone_sidechain() : protocols::cyclic_peptide::PeptideInternalHbondsFilter , protocols::cyclic_peptide::PeptideInternalHbondsMetric
• backbone_sidechain_ : protocols::cyclic_peptide::PeptideInternalHbondsMetric
• 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_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• backbone_stub_linear_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
• backbone_torsions_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• BackboneDB() : protocols::loophash::BackboneDB
• BackboneGridSampler() : protocols::helical_bundle::BackboneGridSampler
• BackboneGridSamplerHelper : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BackboneGridSamplerHelper
• BackboneGridSamplerHelperCOP : protocols::helical_bundle::BackboneGridSampler
• BackboneGridSamplerHelperOP : protocols::helical_bundle::BackboneGridSampler
• BackboneMover() : protocols::simple_moves::BackboneMover
• backbones_ : protocols::loop_grower::LoopPartialSolution
• BackboneSampler() : protocols::enzdes::BackboneSampler
• BackboneSegment() : protocols::loophash::BackboneSegment
• BackboneSegments : protocols::loop_modeler::perturbers::LoopHashPerturber
• BackboneStubConstraint() : core::scoring::constraints::BackboneStubConstraint
• BackboneStubLinearConstraint() : core::scoring::constraints::BackboneStubLinearConstraint
• BackboneTorsionPerturbation() : protocols::hybridization::BackboneTorsionPerturbation
• BackboneTorsionSampler() : protocols::hybridization::BackboneTorsionSampler
• 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 >
• background_prob : core::scoring::func::USOGFunc
• BackgroundEdgeList : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G >
• BackgroundEdgeListConstIter : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
• BackgroundEdgeListIter : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G >
• BackgroundEdgeVector : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G >
• BackgroundEdgeVectorIter : core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G >
• BackgroundNode() : core::pack::interaction_graph::BackgroundNode< V, E, G >
• BackgroundNodeVector : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::FirstClassNode< 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_cdrs() : protocols::antibody::design::GeneralAntibodyModeler
• 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
• backrubmover_ : protocols::backrub::BackrubProtocol , protocols::simple_moves::ShortBackrubMover
• 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
• backward_jump_ : protocols::motifs::Motif
• backward_res_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• BAD : core::scoring::Energies
• bad : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob
• bad_ : protocols::jd2::InnerJob , protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob
• bad_input_jobs_ : protocols::jd2::MPIFileBufJobDistributor
• bad_job_id_ : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• BAD_LOW_PROB : protocols::noesy_assign::CrossPeak
• BAD_SCORE : protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase
• bad_tree() : core::kinematics::EXCN_InvalidFoldTree
• bad_tree_ : core::kinematics::EXCN_InvalidFoldTree
• BalancedKicMover() : protocols::kinematic_closure::BalancedKicMover
• 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
• bAllowPureMovers_ : protocols::environment::Environment
• balls() : core::scoring::packing::PoseBalls
• balls_ : core::pose::xyzStripeHashPose , core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• band : core::scoring::sc::MolecularSurfaceCalculator
• 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
• BareMinimumPDEdge() : core::pack::hbonds::BareMinimumPDEdge
• barrier() : protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver
• base() : protocols::dna::DNAParameters
• Base : protocols::jd2::WriteFileSFB , protocols::toolbox::py_inheritance_test::Base
• base2_xyz() : core::scoring::hbonds::hbtrie::HBAtom
• base2_xyz_ : core::scoring::hbonds::hbtrie::HBAtom
• base5index2symbolString() : core::sequence::ABEGOManager
• base_ : core::scoring::elec::electrie::ElecAtom , core::scoring::lkball::lkbtrie::LKBAtom , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator
• BASE_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• base_ : protocols::antibody_legacy::CDRH3Modeler
• base_analogue() : core::chemical::ResidueTypeBase
• base_analogue_ : core::chemical::ResidueTypeBase
• base_analogue_raw() : core::chemical::ResidueTypeBase
• base_atom_list_ : core::chemical::rna::RNA_Info
• base_atom_name_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• base_atr_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• 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_axis_array_ : core::pose::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_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_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_cutoff_ : core::scoring::rna::RNA_LowResolutionPotential
• base_backbone_z_fade_zone_ : core::scoring::rna::RNA_LowResolutionPotential
• base_base_atom_name_ : protocols::constraint_generator::MetalContactsConstraintGenerator
• base_base_only_ : core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::StackElecEnergy
• base_bin_map_ : protocols::stepwise::screener::BaseBinMapUpdater
• base_centroid_checker_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::BulgeApplier
• base_centroids() : core::scoring::rna::RNA_CentroidInfo
• base_centroids_ : core::scoring::rna::RNA_CentroidInfo
• base_geometry_height_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_geometry_height_array_ : core::pose::rna::RNA_RawBaseBaseInfo
• base_geometry_orientation_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_geometry_orientation_array_ : core::pose::rna::RNA_RawBaseBaseInfo
• base_list_cache_ : core::pack::palette::PackerPalette
• base_movemap_ : protocols::minimization_packing::TaskAwareMinMover
• base_name() : core::chemical::ResidueTypeBase , core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• base_name_ : core::chemical::ResidueTypeBase
• base_native_bonus() : protocols::legacy_sewing::LegacyAssemblyConstraintsMover
• base_native_bonus_ : protocols::legacy_sewing::LegacyAssemblyConstraintsMover , protocols::legacy_sewing::LegacyAssemblyMover
• base_native_pro_bonus_ : protocols::legacy_sewing::LegacyAssemblyConstraintsMover
• base_only() : protocols::dna::RestrictDesignToProteinDNAInterface
• base_only_ : protocols::dna::DnaInterfaceFinder , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::RotamerDNAHBondFilter
• base_pair_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_pair_array_ : core::pose::rna::RNA_RawBaseBaseInfo
• base_pair_axis_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pair_constraint_energy() : core::scoring::constraints::ConstraintEdge
• base_pair_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• base_pair_dist_max_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pair_dist_min_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pair_list() : core::pose::rna::RNA_FilteredBaseBaseInfo
• base_pair_planarity_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pair_rho_max_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pair_rho_min_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pair_rmsd_cutoff() : protocols::recces::options::RECCES_Options
• base_pair_rmsd_cutoff_ : protocols::recces::options::RECCES_Options
• base_pair_rotation_mag() : protocols::recces::options::RECCES_Options
• base_pair_rotation_mag_ : protocols::recces::options::RECCES_Options
• base_pair_score() : core::scoring::dna::DNA_BasePotential
• base_pair_step_ : core::pose::rna::BasePairStep
• base_pair_step_sequence_ : core::import_pose::libraries::BasePairStepSequence
• base_pair_translation_mag() : protocols::recces::options::RECCES_Options
• base_pair_translation_mag_ : protocols::recces::options::RECCES_Options
• base_pair_z_offset_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pairing_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• base_pairs() : core::pose::rna::RNA_SecStruct
• base_pairs_ : core::pose::rna::RNA_SecStruct
• BASE_PARTNER : core::pose::datacache::CacheableDataType
• base_property() : core::chemical::ResidueTypeFinder
• base_property_ : core::chemical::ResidueTypeFinder
• base_pseudo_atom_centers_ : core::scoring::methods::LK_hack
• base_pseudo_atom_f1_f2s_ : core::scoring::methods::LK_hack
• base_rep_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• 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_residue_types_ : core::chemical::ResidueTypeSet
• base_score() : core::scoring::dna::DNA_BasePotential
• base_score_ : core::scoring::disulfides::Cb_Distance_Func
• base_stack_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_stack_array_ : core::pose::rna::RNA_RawBaseBaseInfo
• base_stack_axis_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_stack_axis_array_ : core::pose::rna::RNA_RawBaseBaseInfo
• base_stack_axis_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_stack_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• base_stack_dist_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_stack_list() : core::pose::rna::RNA_FilteredBaseBaseInfo
• base_stack_max_height_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_min_height_ : core::scoring::rna::RNA_LowResolutionPotential
• base_stack_planarity_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• 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::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_stack_z_offset_min_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_stagger_array() : core::pose::rna::RNA_RawBaseBaseInfo
• base_stagger_array_ : core::pose::rna::RNA_RawBaseBaseInfo
• base_state() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• base_state_ : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler
• base_state_lower_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• base_state_upper_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• base_step_energy() : core::scoring::methods::DNA_ReferenceEnergy
• base_step_reference_energies_ : core::scoring::methods::DNA_ReferenceEnergy
• base_step_score() : core::scoring::dna::DNA_BasePotential
• base_string() : core::scoring::dna::DNA_BasePotential
• base_stub_list_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_stubs() : core::scoring::rna::RNA_CentroidInfo
• base_stubs_ : core::scoring::rna::RNA_CentroidInfo
• base_type() : core::chemical::ResidueTypeFinder
• base_type_ : core::chemical::ResidueTypeFinder
• base_type_cop_ : core::chemical::MutableResidueType , core::chemical::ResidueType
• base_types() : core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes
• 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
• base_xyz_ : core::scoring::hbonds::hbtrie::HBAtom
• BaseArchiveManager() : protocols::jd2::archive::BaseArchiveManager
• basebaseAtomIDs : protocols::motifs::Motif
• basebin_ : protocols::match::VoxelSetIterator
• BaseBinMapUpdater() : protocols::stepwise::screener::BaseBinMapUpdater
• BaseCentroidScreener() : protocols::stepwise::screener::BaseCentroidScreener
• 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::calc_taskop_filters::RelativePoseFilter , protocols::simple_filters::DeltaFilter
• baseline_ : protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::Sigmoid , protocols::simple_filters::DeltaFilter
• baseline_checkpointing_filename() : protocols::calc_taskop_filters::Sigmoid
• baseline_checkpointing_filename_ : protocols::calc_taskop_filters::Sigmoid
• baseline_val() : protocols::calc_taskop_filters::RelativePoseFilter
• baseline_val_ : protocols::calc_taskop_filters::RelativePoseFilter
• basenames_ : core::chemical::Selector_BASENAME
• basenames_to_exclude_ : core::pack::task::NOTAA
• basenames_to_keep_ : core::pack::task::PIKAA
• BasePair() : core::pose::rna::BasePair
• basepair() : protocols::dna::DNAParameters
• basepair_axis_stagger_scaling() : core::pose::rna::RNA_FilteredBaseBaseInfo
• basepair_axis_stagger_scaling_ : core::pose::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
• BasePairConstraint() : core::scoring::constraints::BasePairConstraint
• BasePairConstraintCreator() : core::scoring::constraints::BasePairConstraintCreator
• basepairs_ : protocols::dna::DNAParameters
• 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
• baseres_ : protocols::loop_grower::SheetPositions
• 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() : core::pose::rna::BaseStack
• basestack_axis_scaling() : core::pose::rna::RNA_FilteredBaseBaseInfo
• basestack_axis_scaling_ : core::pose::rna::RNA_FilteredBaseBaseInfo
• basestep() : protocols::dna::DNAParameters
• basesteps_ : 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_init_ : protocols::rpc::JSON_RPC
• 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
• BasicDataCache : core::conformation::RotamerSetBase , core::pose::Pose , core::scoring::Energies
• BasicDataCacheOP : core::conformation::RotamerSetBase , core::pose::Pose
• 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_atoms_ : protocols::legacy_sewing::SewResidue
• basis_map() : protocols::sewing::hashing::BasisMapGenerator
• basis_map_ : protocols::sewing::hashing::BasisMapGenerator
• basis_map_from_alignment() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• basis_map_generator() : protocols::sewing::hashing::AlignmentFileGeneratorMover
• basis_map_generator_ : protocols::sewing::hashing::AlignmentFileGeneratorMover , protocols::sewing::movers::AssemblyMover
• basis_pair() : protocols::legacy_sewing::HashEdge
• basis_pair_ : protocols::legacy_sewing::HashEdge , protocols::sewing::data_storage::SmartSegment
• basis_pair_is_valid() : protocols::sewing::hashing::BasisMapGenerator
• basis_resnum : protocols::legacy_sewing::HashValue , protocols::sewing::hashing::HashValue
• basis_segment_id : protocols::sewing::hashing::HashValue
• BasisMapGenerator() : protocols::sewing::hashing::BasisMapGenerator
• Batch() : protocols::jd2::archive::Batch
• batch() : protocols::jd2::archive::Batch , protocols::jd2::JobDistributor
• batch_apply() : protocols::relax::FastRelax
• batch_description_ : protocols::features::ReportToDB
• 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_name_ : protocols::features::ReportToDB
• batch_relax_ : protocols::hybridization::HybridizeProtocol
• batch_relax_absolute_max_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• batch_relax_chunks_ : protocols::loophash::MPI_LoopHashRefine_Master , protocols::mpi_refinement::MPI_Refine_Master
• batch_set_xyz() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::pose::Pose , protocols::environment::ProtectedConformation
• batch_size_ : protocols::loophash::LoopHashMoverWrapper
• batch_underflow() : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::JobDistributor
• batches() : protocols::jd2::archive::BaseArchiveManager
• batches_ : protocols::jd2::archive::BaseArchiveManager , protocols::jd2::JobDistributor
• BatchFeatures() : protocols::features::BatchFeatures
• BatchJobInputter() : protocols::jd2::BatchJobInputter
• BatchList : protocols::abinitio::HedgeArchive , protocols::jd2::archive::BaseArchiveManager
• BatchNrEvaluator() : protocols::simple_filters::BatchNrEvaluator
• BatchStructuresMap : protocols::abinitio::HedgeArchive
• bAutoCut_ : protocols::environment::Environment
• bb : protocols::denovo_design::components::IdealAbegoGenerator , protocols::dna::DnaInterfaceMinMover , protocols::indexed_structure_store::ResidueEntry , protocols::minimization_packing::TaskAwareMinMover , protocols::symmetry::SetupNCSMover
• bb0 : protocols::abinitio::abscript::AtomPack
• bb1 : protocols::abinitio::abscript::AtomPack
• bb2 : protocols::abinitio::abscript::AtomPack
• bb3 : protocols::abinitio::abscript::AtomPack
• bb4 : protocols::abinitio::abscript::AtomPack
• 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::minimization_packing::TaskAwareMinMover , protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::RepGrid , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::symmetry::SetupNCSMover
• bb_acc_avail() : core::scoring::hbonds::HBondResidueMinData
• bb_acc_avail_ : core::scoring::hbonds::HBondResidueMinData
• bb_actions_ : core::select::movemap::MoveMapFactory
• bb_backrub_ : protocols::enzdes::EnzdesBaseProtocol
• bb_bb() : protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::TaskAwareScoreTypeFilter
• bb_bb_ : protocols::protein_interface_design::filters::HbondsToAtomFilter , 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_ : core::pack::interaction_graph::SimpleEdge
• bb_bbE_calced() : core::pack::interaction_graph::SimpleEdge
• bb_bbE_calced_ : core::pack::interaction_graph::SimpleEdge
• BB_BINRANGE : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• bb_bins_from_pose() : protocols::pose_metric_calculators::RotamerRecovery
• bb_boltz_probs() : protocols::mean_field::FlexBBMeanField
• bb_boltz_probs_ : protocols::mean_field::FlexBBMeanField
• bb_boltz_probs_per_aa() : protocols::mean_field::FlexBBMeanField
• bb_boltz_probs_per_aa_ : protocols::mean_field::FlexBBMeanField
• bb_boltz_weights_ : protocols::mean_field::FlexBBMeanField
• 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::pose_metric_calculators::ClashCountCalculator
• bb_clones() : core::conformation::symmetry::SymmetryInfo
• bb_clones_ : core::conformation::symmetry::SymmetryInfo
• bb_comp_db_ : protocols::splice::Splice
• bb_dihedral_tolerance_ : protocols::fldsgn::SheetConstraintGenerator , protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator
• 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_hbonds_graph_ : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• bb_heavy_unsats_ : protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• bb_ids_ : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::MakeRotLibOptionsData , protocols::make_rot_lib::RotData
• bb_index_actions_ : core::select::movemap::MoveMapFactory
• 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_movable_selector() : protocols::fold_from_loops::NubInitioMover
• bb_moves_ : protocols::enzdes::BackboneSampler
• bb_N_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_N_index_ : core::scoring::methods::ResidueCartBondedParameters
• bb_no_extension : protocols::denovo_design::components::IdealAbegoGenerator
• bb_O_index() : core::scoring::methods::ResidueCartBondedParameters
• bb_O_index_ : core::scoring::methods::ResidueCartBondedParameters
• bb_only() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• bb_only_ : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• bb_pair_score() : core::scoring::dssp::Dssp
• bb_pos() : core::scoring::SS_Info
• 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() : 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_ranges_ : protocols::make_rot_lib::MakeRotLibOptionsData
• bb_residues_ : protocols::simple_moves::BBDihedralSamplerMover
• bb_rotamer_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• bb_samplers_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::recces::sampler::rna::MC_RNA_Suite
• bb_sc_carbon_hbond_one_way() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• bb_segs_ : protocols::loop_modeler::perturbers::LoopHashPerturber
• bb_stats() : core::scoring::orbitals::OrbitalsStatistics
• bb_stdev() : protocols::recces::options::RECCES_Options
• bb_stdev_ : protocols::recces::options::RECCES_Options
• bb_tor_out_ : protocols::recces::RECCES_Mover
• bb_torsion_ids_ : protocols::recces::RECCES_Mover
• bbC_ : core::scoring::methods::ProClosureEnergy
• bbCA_ : core::scoring::methods::ProClosureEnergy
• BBClaim() : protocols::topology_broker::claims::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, N >
• bbdep_length_parameters() : core::scoring::methods::ResidueCartBondedParameters
• bbdep_length_params_ : core::scoring::methods::ResidueCartBondedParameters
• bbdep_nrc_interpdata_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbdep_nrchi_binsize_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbdep_nrchi_nbins_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbdep_nrchi_sample() : core::pack::dunbrack::BBDepSemiRotamericData< T, N >
• bbdep_nrchi_sample_ : core::pack::dunbrack::BBDepSemiRotamericData< T, N >
• bbdep_nrchi_score() : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbdep_rotamers_to_sample_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbdep_rotsample_sorted_order_ : 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
• BBdisplay_state : protocols::viewer::GraphicsState
• bbdof_list : protocols::splice::ResidueBBDofs
• BBDofs() : protocols::splice::BBDofs
• bbdofs() : protocols::splice::ResidueBBDofs
• bbdofs_ : protocols::splice::ResidueBBDofs
• BBG8T3AMover() : protocols::simple_moves::BBG8T3AMover
• bbg_move_prob_ : protocols::protein_interface_design::movers::BackrubDDMover
• BBGaussianMover() : protocols::simple_moves::BBGaussianMover
• bbgmover_ : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• 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_non_rotameric_chi_scores_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbind_nrchi_binsize_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbind_nrchi_nbins_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbind_nrchi_sample() : core::pack::dunbrack::BBIndSemiRotamericData< T, N >
• bbind_nrchi_sample_ : core::pack::dunbrack::BBIndSemiRotamericData< T, N >
• bbind_nrchi_sampling_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbind_nrchi_scoring_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbind_rotamers_sorted_by_probability_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >
• bbind_rotamers_to_sample_ : core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< 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 >
• bbl_ : protocols::scoring::ImplicitFastClashCheck
• bbl_ca_ : protocols::scoring::ImplicitFastClashCheck
• bblock_dist_ : protocols::matdes::BuildingBlockInterfaceOperation
• bblock_reference_pose_ : protocols::matdes::BuildingBlockInterfaceOperation
• bbM1 : protocols::abinitio::abscript::AtomPack
• BBMatching() : protocols::splice::BBMatching
• bbmove_ : protocols::hybridization::CartesianSampler
• bbN_ : core::scoring::methods::ProClosureEnergy
• bbnbrs() : protocols::evolution::NucleotideMutation
• bbnbrs_ : protocols::evolution::NucleotideMutation
• bbO_ : core::scoring::methods::ProClosureEnergy
• bbox_padding_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• bbpos_is_set() : protocols::fldsgn::topology::SS_Info2
• bbpos_is_set_ : protocols::fldsgn::topology::SS_Info2
• BBrms : protocols::loophash::FilterBucket
• bbs_ : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::RotData
• 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 , core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• BBTorsionSRFDOP : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• bbx1_ : protocols::sic_dock::scores::MotifHashRigidScore
• bbx2_ : protocols::sic_dock::scores::MotifHashRigidScore
• bbx_ : protocols::sic_dock::scores::TrisBpyScore
• bCentroid_ : protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• bcfl : core::scoring::APBSConfig::I_PARAM
• bckg() : core::scoring::epr_deer::DEERDecayData
• bckg_ : core::scoring::epr_deer::FittingInfo
• 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
• bdx : core::scoring::packstat::LR_MP_AtomData
• bdy : core::scoring::packstat::LR_MP_AtomData
• be_lenient() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• be_lenient_ : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• bead_bead_interaction : core::scoring::etable::AtomPairEnergy
• beamscorecutoff_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::LoopPartialSolutionStore
• beamwidth_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• become() : protocols::sewing::data_storage::SmartSegment , protocols::sewing::data_storage::SmartSewingResidue
• before : protocols::denovo_design::task_operations::SurroundingSS
• before_chain_break_grid_index_screening : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• before_minimization_reference_energies_ : protocols::optimize_weights::IterativeOptEDriver
• 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::Extent< PageIterator > , 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::palette::BaseTypeList , 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 , core::select::PreSelectedResidRange , protocols::abinitio::abscript::ResidueChunkSelection , protocols::abinitio::PairingStatistics , protocols::abinitio::Templates , protocols::constraint_generator::ConstraintsMap , protocols::denovo_design::task_operations::AAFrequencies , protocols::dna::DnaChains , protocols::features::Segment , protocols::filters::CompoundFilter , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::StrandPairingSet , protocols::forge::build::BuildManager , protocols::forge::remodel::RemodelWorkingSet , 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
• 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::parser::FragmentReader , protocols::pose_metric_calculators::FragQualCalculator
• begin_const() : core::io::raw_data::RawFileData
• begin_critical_section() : protocols::jd2::BOINCJobDistributor , protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor
• begin_native_ : protocols::protein_interface_design::filters::RmsdFilter
• begin_pose_ : protocols::protein_interface_design::filters::RmsdFilter
• 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
• behavior_ : core::pack::task::operation::AddBehaviorRLT
• behavior_non_catalytic_ : protocols::enzdes::SetCatalyticResPackBehavior
• behaviors_ : core::pack::task::ResidueLevelTask_
• behaviour_ : protocols::helical_bundle::BundleReporterFilter
• 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
• being_packed_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• below_distance_threshold_ : protocols::pose_length_moves::PossibleLoop
• bEnableCcdMoves_ : protocols::loops::loop_closure::ccd::LoopClosure
• benchmark_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::CloseOneCDRLoop , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3CterInsert , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::CloseOneMover , protocols::antibody_legacy::GraftMover , protocols::antibody_legacy::GraftOneMover , protocols::antibody_legacy::LoopRlxMover
• BenchmarkBuildRotamersMover() : protocols::testing::BenchmarkBuildRotamersMover
• bend() : protocols::fldsgn::topology::Helix
• bend_ : protocols::fldsgn::topology::Helix
• bend_angle() : protocols::fldsgn::filters::HelixPairingFilter
• bend_angle_ : protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• bend_level() : protocols::fldsgn::filters::StrandCurvatureByLevels
• bend_level_ : protocols::fldsgn::filters::StrandCurvatureByLevels
• bEnumeratedLastTime_ : protocols::abinitio::IterativeBase
• Berendsen_Integrator() : protocols::md::CartesianMD
• BesselI0() : core::scoring::CenHBPotential
• best_ : core::optimization::GA_Minimizer , protocols::simple_moves::sidechain_moves::SidechainMCMover
• best_abs_log_norm_ratio() : core::optimization::SimpleDerivCheckResult , core::optimization::symmetry::MinDebug
• best_abs_log_norm_ratio_ : core::optimization::SimpleDerivCheckResult
• best_assembly_ : protocols::sewing::movers::AssemblyMover
• 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_center_ : protocols::membrane::OptimizeMembranePositionMover
• best_combine_score_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• best_complete_assembly_ : protocols::legacy_sewing::LegacyGreedyAssemblyMover
• best_cos_theta() : core::optimization::SimpleDerivCheckResult , core::optimization::symmetry::MinDebug
• best_cos_theta_ : core::optimization::SimpleDerivCheckResult
• best_cyclic_pep_start : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::CyclizedReportInfo
• best_cyclic_peptides_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::CyclizedReportInfo
• best_energy_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• best_entities() : protocols::genetic_algorithm::GeneticAlgorithmBase
• best_entity_ : protocols::pack_daemon::PackDaemon
• best_entity_positive_states_ : protocols::multistate_design::MultiStateFitnessFunction
• best_exemplar : protocols::cluster::DataPoint
• best_fit() : core::scoring::epr_deer::DEERDistanceDistribution
• best_fit_ : core::scoring::epr_deer::DEERDistanceDistribution
• best_fitness_ : protocols::multistate_design::MultiStateFitnessFunction
• best_fitness_from_current_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• best_fragment_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• best_geometry_score_ : protocols::sewing::hashing::LigandBindingResPlacer
• best_grid_point_ : core::scoring::nmr::NMRGridSearch
• best_Kmer_rms() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• best_ligands_ : protocols::ligand_docking::TransformEnsemble
• best_linear_peptides_ : protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter
• best_match_dspos1s_ : protocols::match::output::BestMatchesCollection
• best_matches_ : protocols::match::output::BestMatchesCollection
• best_motif : core::scoring::motif::XformSummary
• 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::SimpleDerivCheckResult , core::optimization::symmetry::MinDebug
• best_norm_analytic_ : core::optimization::SimpleDerivCheckResult
• best_norm_numeric() : core::optimization::SimpleDerivCheckResult , core::optimization::symmetry::MinDebug
• best_norm_numeric_ : core::optimization::SimpleDerivCheckResult
• best_normal_ : protocols::membrane::OptimizeMembranePositionMover
• 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::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_rotamers_ : protocols::motifs::BuildPosition
• best_score() : protocols::multistate_design::SingleState , protocols::relax::SRelaxPose
• best_score_ : core::io::pose_from_sfr::GeometricRenameIsomorphismCallback , protocols::legacy_sewing::LegacyGreedyAssemblyMover , 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
• best_z_ : protocols::membrane::OptimizeMembranePositionMover
• bestClusMargin : protocols::cluster::calibur::Clustering
• bestClusSize : protocols::cluster::calibur::Clustering
• 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::io::CrystInfo , core::pose::Pose , core::scoring::CSA , protocols::cryst::Spacegroup , protocols::dna::DNABase , protocols::protein_interface_design::Transformation , protocols::stepwise::sampler::rigid_body::EulerAngles , Transformation
• beta_ : core::io::CrystInfo , core::scoring::CSA , core::scoring::nmr::NMRTensor , protocols::cryst::Spacegroup , protocols::dna::DNABase , protocols::simple_filters::AbinitioBaseFilter , protocols::stepwise::sampler::rigid_body::EulerAngles
• beta_aform() : core::chemical::rna::RNA_FittedTorsionInfo
• beta_atom_names_ : core::scoring::dna::DNATorsionPotential
• beta_components() : core::scoring::dna::DNATorsionPotential
• beta_components_ : core::scoring::dna::DNATorsionPotential
• beta_id_i_ : protocols::features::strand_assembly::StrandFragment
• beta_id_j_ : protocols::features::strand_assembly::StrandFragment
• beta_potential_ : core::scoring::rna::RNA_TorsionPotential
• beta_ratio_ : protocols::simple_filters::AbinitioBaseFilter
• beta_turn_distance_cutoff() : protocols::features::BetaTurnDetection
• beta_turn_distance_cutoff_ : protocols::features::BetaTurnDetection
• beta_turn_length() : 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
• betamax : core::pose::rna::RNA_SuiteName
• betamin : core::pose::rna::RNA_SuiteName
• BetaSheetArchitect() : protocols::denovo_design::architects::BetaSheetArchitect
• BetaTurnDetection() : protocols::features::BetaTurnDetection
• BetaTurnDetectionFeatures() : protocols::features::BetaTurnDetectionFeatures
• bExclusive_ : protocols::topology_broker::RigidChunkClaimer
• bF() : protocols::frag_picker::VallResidue
• bF_ : protocols::frag_picker::VallResidue
• bfac() : core::scoring::motif::Xfrag , core::scoring::packing::PoseBalls , core::scoring::packstat::SimplePDB_Atom
• bfac1() : core::scoring::motif::ResPairMotif
• bfac1_ : core::scoring::motif::ResPairMotif
• bfac2() : core::scoring::motif::ResPairMotif
• bfac2_ : core::scoring::motif::ResPairMotif
• bfac_ : core::scoring::motif::Xfrag , core::scoring::packing::PoseBalls
• 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
• bForceSingleSheet_ : protocols::jumping::SheetBuilder
• bFullatom_ : protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• bg() : protocols::toolbox::ScoreRmsPoints
• bg_ : protocols::toolbox::ScoreRmsPoints
• 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::func::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::NPDHBondInteractionGraph< 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 > , core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >
• bg_residues_ : core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc
• bg_sd_ : core::scoring::func::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::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• bgtfce_mark_edge_for_deletion() : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• bgtfce_marked_for_deletion() : core::pack::interaction_graph::BackgroundToFirstClassEdge< 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
• bias : protocols::environment::claims::CutBiasElement
• bias_energy() : protocols::canonical_sampling::BiasedMonteCarlo
• bias_energy_ : protocols::canonical_sampling::BiasedMonteCarlo , protocols::canonical_sampling::HamiltonianExchange
• bias_grid_ : protocols::canonical_sampling::BiasEnergy
• bias_sampling_ : protocols::minimization_packing::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• biased_mainchain_torsions() : core::scoring::bin_transitions::BinTransitionCalculator
• BiasedFragmentMover() : protocols::nonlocal::BiasedFragmentMover
• BiasedMonteCarlo() : protocols::canonical_sampling::BiasedMonteCarlo
• BiasEnergy() : protocols::canonical_sampling::BiasEnergy
• biases_ : protocols::environment::claims::CutBiasClaim
• BiasVector : protocols::environment::EnvClaimBroker
• 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::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• big_polar_h_ : core::scoring::sasa::SasaCalc
• bigbin() : protocols::frags::VallData
• bigbin_ : protocols::frags::VallData
• BigBinConstraint() : core::scoring::constraints::BigBinConstraint
• BigBinConstraintCreator() : core::scoring::constraints::BigBinConstraintCreator
• bIgnoreSequenceSeparation() : protocols::abinitio::FoldConstraints
• bIgnoreSequenceSeparation_ : protocols::abinitio::FoldConstraints
• bin() : core::scoring::constraints::BigBinConstraint , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• BIN : protocols::sic_dock::SICFast
• bin0_of_real() : core::scoring::motif::ResPairMotifMetaBinner
• Bin3D : protocols::match::Bool3DGrid , protocols::match::Bool3DGridKinemageWriter , protocols::match::BumpGrid
• Bin6D : protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::VoxelSetIterator
• bin_ : core::scoring::constraints::BigBinConstraint , protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• 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_count_ : protocols::ligand_docking::ComputeLigandRDF
• bin_definition_exists() : core::scoring::bin_transitions::BinTransitionCalculator
• BIN_EQUIVALENTS : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• 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_i_cdf_given_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• bin_index() : core::scoring::motif::MotifHash , core::scoring::motif::XformScore
• bin_index_() : protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::TorsionBinSimilarity
• bin_index_hasher : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• bin_iplus1_cdf_given_i_ : core::scoring::bin_transitions::BinTransitionData
• bin_matches() : core::pack::dunbrack::DunbrackConstraint
• bin_max_ : core::pose::rna::VDW_Grid , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• bin_min_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• bin_name() : core::select::residue_selector::BinSelector
• bin_name_ : core::select::residue_selector::BinSelector
• bin_names_ : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• bin_offset_ : core::pose::rna::VDW_Grid , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• bin_params_file_ : core::scoring::bin_transitions::BinTransitionCalculator
• bin_params_file_name() : core::select::residue_selector::BinSelector
• bin_params_file_name_ : core::select::residue_selector::BinSelector
• bin_params_loaded() : core::scoring::bin_transitions::BinTransitionCalculator
• bin_params_loaded_ : core::scoring::bin_transitions::BinTransitionCalculator
• bin_probs_ : protocols::frag_picker::quota::ABEGO_SS_Config
• bin_rotameric_chi() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• bin_size_ : core::scoring::func::SplineFunc , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::ncbb::SecStructFinder , protocols::scoring::methods::saxs::PDDFEnergy , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• bin_squared_ : protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• bin_transition_calculator_ : core::select::residue_selector::BinSelector , protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins
• bin_transition_data() : core::scoring::bin_transitions::BinTransitionCalculator
• bin_transition_data_ : core::scoring::bin_transitions::BinTransitionCalculator
• 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_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_output_ : core::io::silent::SilentFileOptions
• binary_rna_output() : core::import_pose::options::RNA_DeNovoProtocolOptions
• 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_data : protocols::ligand_docking::ProtLigPair_info
• bind_vec_constraint() : protocols::antibody::AntibodyDatabaseManager
• binder_finders_ : protocols::sewing::movers::LigandBindingAssemblyMover
• binder_selector() : protocols::fold_from_loops::utils::Nub
• binder_selector_ : protocols::fold_from_loops::utils::Nub , protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter
• binder_weight() : protocols::fold_from_loops::NubInitioMover
• binding() : protocols::residue_optimization::MetapatchEnumeration
• binding_cycles_ : protocols::sewing::movers::LigandBindingAssemblyMover
• binding_E_ : protocols::dna::DnaInterfacePacker
• binding_energy_values_ : core::scoring::rna::data::RNA_DMS_Potential
• BindingSiteConstraint() : protocols::constraints_additional::BindingSiteConstraint
• BindingSiteConstraintCreator() : protocols::constraints_additional::BindingSiteConstraintCreator
• BindingStrainFilter() : protocols::protein_interface_design::filters::BindingStrainFilter
• bindis_ : protocols::simple_moves::AtomHash
• binfile_ : protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins
• binfile_loaded_ : protocols::simple_moves::bin_transitions::InitializeByBins , protocols::simple_moves::bin_transitions::PerturbByBins
• bInheritCuts_ : protocols::environment::Environment
• bInit_ : protocols::abinitio::hConvergenceCheck , protocols::hybridization::hConvergenceCheck
• bInitDofs_ : protocols::topology_broker::FragmentClaimer
• bInitialize_ : protocols::abinitio::abscript::FragmentCM
• 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
• binnames_i_ : core::scoring::bin_transitions::BinTransitionData
• binnames_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• binner() : protocols::match::HitHasher
• binner_ : protocols::match::HitNeighborFinder , protocols::match::MatchCounter
• binranges_i_ : core::scoring::bin_transitions::BinTransitionData
• binranges_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• bins_ : core::pose::rna::VDW_Grid
• bins_per_A2 : core::scoring::etable::EtableOptions
• bins_per_A2_ : core::scoring::etable::Etable
• bins_per_angstrom() : core::scoring::epr_deer::DEERData
• bins_per_angstrom_ : core::scoring::epr_deer::DEERData
• BINS_PER_ANGSTROM_ : core::scoring::epr_deer::DEERIO
• bins_vect_ : core::scoring::func::SplineFunc
• bins_vect_size_ : core::scoring::func::SplineFunc
• BinSelector() : core::select::residue_selector::BinSelector
• binsizes_ : core::chemical::NCAARotLibNumRotamerBins
• binsums_i() : core::scoring::bin_transitions::BinTransitionData
• binsums_i_ : core::scoring::bin_transitions::BinTransitionData
• binsums_i_cdf_ : core::scoring::bin_transitions::BinTransitionData
• binsums_iplus1() : core::scoring::bin_transitions::BinTransitionData
• binsums_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• binsums_iplus1_cdf_ : core::scoring::bin_transitions::BinTransitionData
• BinTransitionCalculator() : core::scoring::bin_transitions::BinTransitionCalculator
• BinTransitionData() : core::scoring::bin_transitions::BinTransitionData
• binw_ : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• binwidth_ : core::scoring::loop_graph::evaluator::SixDTransRotPotential
• binwidth_dist : core::scoring::sc::MolecularSurfaceCalculator
• binwidth_norm : core::scoring::sc::MolecularSurfaceCalculator
• BIOLOGICAL_UNIT : core::io::HeaderInformation
• BIOPConstIterator : protocols::forge::build::BuildManager , protocols::forge::components::VarLengthBuild
• BIOPIterator : protocols::forge::build::BuildManager
• bitmask_for_position() : protocols::match::OccupiedSpaceHash
• Bjump_ : protocols::cryst::DockLatticeMover
• bJumps_use_IntraResStub_ : core::io::silent::BinarySilentStruct , 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::FragmentJumpClaimer
• 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
• blank() : core::pose::rna::RNA_SecStruct
• blank_score_terms() : protocols::recces::options::RECCES_Options
• 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 >
• blast_pgp_ : protocols::frag_picker::FragmentScoreFilter
• blastp_identity_cutoff_ : protocols::tcr::TCRmodel
• bLocal_ : protocols::topology_broker::CoordConstraintClaimer
• block() : protocols::jd2::SingleFileBuffer , protocols::jd2::WriteFileSFB
• block_file() : protocols::jd2::MpiFileBuffer
• block_signals() : core::conformation::Conformation , protocols::denovo_design::components::StructureData
• block_signals_ : protocols::denovo_design::components::StructureData
• block_stack() : protocols::recces::options::RECCES_Options
• block_stack_ : protocols::recces::options::RECCES_Options
• block_stack_above_res() : core::import_pose::RNA_DeNovoParameters , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• block_stack_above_res_ : core::import_pose::FullModelPoseBuilder , core::import_pose::RNA_DeNovoParameters , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• block_stack_below_res() : core::import_pose::RNA_DeNovoParameters , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• block_stack_below_res_ : core::import_pose::FullModelPoseBuilder , core::import_pose::RNA_DeNovoParameters , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• blocked_files_ : protocols::jd2::MpiFileBuffer
• blocking_signals() : core::conformation::Conformation
• Blosum62Map() : core::sequence::Blosum62Map
• BLOSUM_62 : protocols::sparta::Sparta::SpartaLib
• blosum_history_ : protocols::legacy_sewing::Assembly
• blosum_matrix_ : protocols::frag_picker::scores::ProfileScoreBlosum62
• BlosumMatrix : protocols::sparta::Sparta::SpartaLib
• BluePrint : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FlxbbDesign
• blueprint : protocols::forge::remodel::RemodelData
• BluePrint() : protocols::parser::BluePrint , protocols::task_operations::DsspDesignOperation
• blueprint_ : protocols::denovo_design::architects::BlueprintArchitect , protocols::denovo_design::filters::SSPredictionFilter , protocols::fldsgn::BluePrintBDR , protocols::flxbb::FlxbbDesign , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelMover , protocols::parser::FragmentReader , protocols::task_operations::DsspDesignOperation
• blueprint_cst_definition() : protocols::forge::remodel::RemodelEnzdesCstModule
• BlueprintArchitect() : protocols::denovo_design::architects::BlueprintArchitect
• BluePrintBDR() : protocols::fldsgn::BluePrintBDR
• BluePrintOP : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintGenerator , protocols::flxbb::FlxbbDesign , protocols::task_operations::DsspDesignOperation
• bMinTrial_ : protocols::abinitio::FoldConstraints
• bNoRecoverLowAtSwitch_ : protocols::abinitio::ConstraintFragmentSampler
• BOGUS_ASSIGNMENTS : protocols::noesy_assign::PeakAssignmentResidueMap
• BOGUS_ATOM_ID() : core::id::AtomID
• BOGUS_BATCH_ID : protocols::jd2::BatchJobInputter
• 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
• bohr : core::scoring::MultipoleElecPotential
• Boinc() : protocols::boinc::Boinc
• boinc_mode_ : protocols::canonical_sampling::CanonicalSamplingMover
• BoincCurrentPoseObserver() : protocols::boinc::BoincCurrentPoseObserver
• BOINCJobDistributor() : protocols::jd2::BOINCJobDistributor
• boltz_rank() : protocols::monte_carlo::GenericMonteCarloMover
• boltz_rank_ : protocols::monte_carlo::GenericMonteCarloMover
• boltz_temp_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• 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_choice_post_enumerated_minimize_ : protocols::stepwise::options::StepWiseBasicOptions
• boltzmann_factor_ : core::scoring::nmr::NMRSpinlabel
• boltzmann_kbt_ : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• boltzmann_result() : protocols::monte_carlo::GenericSimulatedAnnealer
• boltzmann_rotamer_mover_ : protocols::simple_moves::CoupledMover
• BoltzmannFilter() : protocols::protein_interface_design::filters::BoltzmannFilter
• BoltzmannRotamerMover() : protocols::minimization_packing::BoltzmannRotamerMover
• Bond() : core::chemical::Bond
• bond() : core::chemical::MutableResidueType
• 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_list_ : protocols::rna::movers::ErraserMinimizerMover
• bond_angle_map_ : protocols::backrub::BackrubMover
• bond_angle_residue_type_param_set() : core::scoring::methods::EnergyMethodOptions , protocols::branch_angle::BranchAngleOptimizer
• bond_angle_residue_type_param_set_ : core::scoring::methods::EnergyMethodOptions , protocols::branch_angle::BranchAngleOptimizer
• bond_angle_sd_ : protocols::simple_moves::ConstrainToIdealMover
• bond_angle_sd_polar_hydrogen_ : protocols::simple_moves::ConstrainToIdealMover
• bond_angles_ : protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::perturbers::LogFilePerturber
• bond_assigned_ : protocols::cyclic_peptide::PeptideCyclizeMover
• bond_geometry_energy() : core::scoring::constraints::ConstraintEdge
• bond_geometry_energy_ : core::scoring::constraints::ConstraintEdge
• bond_iterators() : core::chemical::MutableResidueType
• bond_length() : core::conformation::Conformation , core::kinematics::AtomTree , protocols::simple_moves::CutChainMover
• bond_length_ : protocols::simple_moves::CutChainMover
• bond_length_dof_id() : core::kinematics::AtomTree
• bond_length_sd_ : protocols::simple_moves::ConstrainToIdealMover
• bond_length_sd_polar_hydrogen_ : protocols::simple_moves::ConstrainToIdealMover
• bond_lengths_ : core::chemical::IdealBondLengthSet , protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::perturbers::LogFilePerturber
• bond_lookup_ : core::scoring::GenericBondedPotential
• bond_name() : core::chemical::Bond
• bond_name_ : core::chemical::Bond
• bond_orientation() : core::conformation::Conformation
• bond_pot_ : core::scoring::GenericBondedPotential
• bond_ringness() : core::chemical::ResidueType
• bond_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
• bond_string_to_sdf_size_ : core::chemical::mmCIF::mmCIFParser
• bond_torsion_sd_ : protocols::simple_moves::ConstrainToIdealMover
• bond_torsion_sd_polar_hydrogen_ : protocols::simple_moves::ConstrainToIdealMover
• bond_type() : core::chemical::ResidueType
• bond_type_ : core::chemical::AddBondType
• 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
• bondangle_perturbation_magnitude_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• bondangle_solutions_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• BondAngleKey : protocols::backrub::BackrubSegment
• bondangles_actions_ : core::select::movemap::MoveMapFactory
• 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
• bonded2() : core::chemical::AutomorphismIterator
• bonded_atom_list_ : protocols::rna::movers::ErraserMinimizerMover
• bonded_heavyatoms() : core::chemical::MutableResidueType
• bonded_hydrogens() : core::chemical::MutableResidueType
• bonded_neighbor() : core::chemical::ResidueType , core::conformation::Residue
• bonded_neighbor_ : core::chemical::ResidueType
• bonded_neighbor_all_res() : core::conformation::Conformation
• bonded_neighbor_iterators() : core::chemical::MutableResidueType
• bonded_neighbor_ringness_ : core::chemical::ResidueType
• bonded_neighbor_ringnesses() : core::chemical::ResidueType
• bonded_neighbor_type_ : core::chemical::ResidueType
• bonded_neighbor_types() : core::chemical::ResidueType
• bonded_neighbors() : core::chemical::MutableResidueType
• bonded_orbitals() : core::chemical::Atom , core::chemical::ResidueType , core::conformation::Residue
• bonded_orbitals_ : core::chemical::Atom , core::chemical::ResidueType
• BondedAtom() : core::kinematics::tree::BondedAtom
• BondedResidueSelector() : core::select::residue_selector::BondedResidueSelector
• BondID() : core::id::BondID
• BondInfo() : protocols::denovo_design::components::BondInfo
• bondlen_precision_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• bondlength_perturbation_magnitude_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• bondlength_solutions_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• bondlengths_actions_ : core::select::movemap::MoveMapFactory
• 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
• bondnos_ : core::scoring::ResidueExclParams
• bonds() : core::chemical::ResidueType
• bonds_scorefxn_ : protocols::seeded_abinitio::SegmentHybridizer
• bondType : core::chemical::sdf::BondData
• bonus_ : core::pack::dunbrack::DunbrackConstraint , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle
• bonus_function() : core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy
• bonus_map_ : core::scoring::constraints::ResidueTypeLinkingConstraint
• bonus_score_ : protocols::loop_grower::LoopPartialSolution
• bonus_value() : protocols::hotspot_hashing::HotspotStub
• bonus_value_ : protocols::hotspot_hashing::HotspotStub
• bonus_wtd_ : protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy
• 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::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::concepts::Library< Books > , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallLibrary
• BookIterator : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::concepts::Library< Books > , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallLibrary
• 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 >
• bookmarks() : core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• Bookmarks : core::fragment::picking_old::vall::VallLibrarian
• 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
• BoolDataCacheBoolOP : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• boolean_parameter() : core::conformation::parametric::ParametrizationCalculator
• boolean_parameter_cop() : core::conformation::parametric::ParametrizationCalculator
• BooleanValuedParameter() : core::conformation::parametric::BooleanValuedParameter
• BoolVector : core::select::residue_selector::CachedResidueSubset
• BoolVectorOP : core::select::residue_selector::CachedResidueSubset
• 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::stepwise::modeler::rna::StepWiseRNA_CountStruct
• both_criteria_needed_to_pass_ : protocols::match::NumNeighborsMPM
• both_remnants_would_be_deleted() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• BOTH_SC_AND_BB : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• bottom() : protocols::dna::DnaPosition
• bottom_ : protocols::dna::DnaPosition
• bound() : protocols::simple_filters::NonSequentialNeighborsFilter
• bound_ : protocols::optimize_weights::DGBindOptEData , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::task_operations::ProteinCore
• bound_energies_ : protocols::simple_ddg::ddG
• bound_HOH_ : protocols::simple_ddg::ddG
• bound_HOH_V_ : protocols::simple_ddg::ddG
• bound_mut_db_reporter_ : protocols::features::InterfaceDdGMover
• bound_mut_pose_ : protocols::features::InterfaceDdGMover
• bound_mut_score_ : protocols::features::InterfaceDdGMover
• bound_per_residue_energies_ : protocols::simple_ddg::ddG
• bound_rmsd_ : protocols::simple_ddg::ddG
• bound_rmsd_super_ : protocols::simple_ddg::ddG
• bound_struct() : protocols::optimize_weights::DGBindOptEData
• bound_width() : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• bound_width_ : protocols::constraint_movers::AddConstraintsToCurrentConformationMover
• bound_wt_db_reporter_ : protocols::features::InterfaceDdGMover
• bound_wt_pose_ : protocols::features::InterfaceDdGMover
• bound_wt_score_ : protocols::features::InterfaceDdGMover
• boundaries() : core::conformation::membrane::AqueousPoreParameters
• boundaries_ : core::conformation::membrane::AqueousPoreParameters
• boundary_ : core::scoring::loop_graph::evaluator::SixDTransRotPotential , protocols::task_operations::SelectBySASAOperation
• boundary_his_must_to_hbond_pos_charge_ : protocols::hbnet::HBNetStapleInterface
• boundary_left() : core::kinematics::FoldTree
• boundary_neighs() : core::scoring::elec::FAElecContextData
• boundary_neighs_ : core::scoring::elec::FAElecContextData
• boundary_residues_ : protocols::hbnet::HBNet
• boundary_right() : core::kinematics::FoldTree
• boundary_selector_ : protocols::hbnet::HBNet
• boundbox() : core::scoring::atomic_depth::AtomicDepth
• bounded() : protocols::relax::AtomCoordinateCstMover
• bounded_ : protocols::constraint_generator::CoordinateConstraintGenerator , protocols::constraint_generator::HydrogenBondConstraintGenerator , protocols::relax::AtomCoordinateCstMover
• bounded_protocol() : protocols::frag_picker::FragmentPicker
• bounded_width_ : protocols::constraint_generator::CoordinateConstraintGenerator
• 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 >
• 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
• boundingatom() : core::scoring::atomic_depth::AtomicDepth
• BoundingBox : protocols::match::Bool3DGrid , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::OccupiedSpaceHash , protocols::match::VoxelSetIterator , protocols::nmr::pcs::PCSLigandTransformMover
• BoundingSphere : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• bounds() : core::scoring::epr_deer::DEERDistanceBounds
• bounds_ : core::scoring::epr_deer::DEERDistanceBounds
• bounds_check_entity() : protocols::pack_daemon::EntityCorrespondence
• bounds_check_residue() : protocols::pack_daemon::EntityCorrespondence
• bOverlapChainbreaks_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::KinematicAbinitio
• box_size : protocols::ligand_docking::Transform_info , protocols::ligand_docking::TransformEnsemble_info
• boxes_per_dimension : protocols::sewing::hashing::HasherSettings
• boxlength_ : core::scoring::atomic_depth::AtomicDepth
• bp_motifhits() : protocols::motifs::MotifSearch
• bp_res() : protocols::recces::params::RECCES_Parameters
• bp_res_ : protocols::recces::params::RECCES_Parameters
• bp_rotamers() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• BP_type : core::scoring::dna::DNA_BasePotential
• bpdata_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• bpdata_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• bps_moves() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• bps_moves_ : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::rna::denovo::RNA_DeNovoPoseInitializer
• bQuickTest() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• bQuickTest_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• BR() : core::scoring::FACTSResidueInfo
• BR_ : core::scoring::FACTSResidueInfo
• bRampChainbreak_ : protocols::loops::loop_closure::ccd::LoopClosure
• bRampChainbreaks_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::KinematicAbinitio
• bRampCoordConstraints_ : protocols::abinitio::ConstraintFragmentSampler
• branch_atom_ : core::scoring::methods::GoapRsdType
• 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_length_ : protocols::evolution::EvolutionaryDynamicsMover
• branch_lower_termini_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• branch_lower_termini_extra_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• branch_overlapping_networks() : protocols::hbnet::HBNet
• branch_point() : core::chemical::carbohydrates::CarbohydrateInfo
• branch_points_ : core::chemical::carbohydrates::CarbohydrateInfo
• branch_tips_ : core::conformation::carbohydrates::GlycanTree
• 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
• branches_actions_ : core::select::movemap::MoveMapFactory
• branchopt() : protocols::backrub::BackrubMover
• branchopt_ : protocols::backrub::BackrubMover
• BranchParam1() : protocols::branch_angle::BranchParam1
• BranchParam2() : protocols::branch_angle::BranchParam2
• bRandomSheet_ : protocols::topology_broker::TemplateJumpClaimer
• breadth_first_connect() : protocols::loop_grower::DensSkeleton
• break_a_disulfide() : protocols::simple_moves::MutateResidue
• break_disulfide_bonds() : protocols::simple_moves::MutateResidue
• break_disulfide_bonds_ : protocols::simple_moves::MutateResidue
• break_disulfides() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• break_repack_reform() : protocols::minimization_packing::DisulfideOptimizationMover
• break_side() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• break_side_ : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• break_side_ramp() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• break_side_ramp_ : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• break_side_ramp_value_ : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• breaks_skeleton() : protocols::loop_grower::DensSkeleton
• bRegenerateFromInputPose_ : protocols::topology_broker::CoordConstraintClaimer
• bRelative_ : protocols::environment::claims::XYZClaim
• 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_ : protocols::denovo_design::connection::ConnectionArchitect
• bridge_res() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• bridge_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• BridgeChainsMover() : protocols::denovo_design::movers::BridgeChainsMover
• brief : update_ResidueType_enum_files.EnumInfo
• bRigidInRelax_ : protocols::topology_broker::RigidChunkClaimer
• bring_to_origin() : protocols::simple_filters::ResidueDepthCalculator
• broadcast_entity_string() : protocols::pack_daemon::MPIMultistateFitnessFunction
• broker() : protocols::environment::Environment , protocols::topology_broker::TopologyClaimer
• 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
• BrokeredJumpDataCOP : protocols::environment::EnvClaimBroker
• BrokeredJumpDataOP : protocols::environment::EnvClaimBroker
• broking() : protocols::topology_broker::TopologyBroker
• broking_finished() : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::environment::ClientMover
• 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::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• brute_move_small() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• 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
• 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
• bSuperimpose_ : protocols::topology_broker::CoordConstraintClaimer
• btd_ : protocols::features::BetaTurnDetectionFeatures
• btmplt() : protocols::tcr::TCRmodel
• btmplt_ : protocols::tcr::TCRmodel
• buckle() : protocols::dna::DNABasepair
• buckle_ : protocols::dna::DNABasepair
• buf : protocols::sparta::ANN , protocols::sparta::GDB , protocols::sparta::Sparta::SpartaLib
• buf_ : core::io::serialization::BUFFER
• buf_to_address() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• BUFFER() : core::io::serialization::BUFFER
• buffer_factor_ : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• buffer_length_ : protocols::simple_moves::WobbleMover
• buffer_limit() : protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification
• buffer_limit_ : protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter , protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification , protocols::jd3::pose_outputters::SilentFilePoseOutputter
• buffer_observers() : core::pose::Pose
• buffer_rank_ : protocols::jd2::MpiFileBuffer
• buffer_signals() : core::conformation::Conformation
• BUFFER_SIZE : protocols::wum::WorkUnitBase::WU_Header
• buffered_lores_structs_ : protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter
• buffered_structs_ : protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter , protocols::jd3::pose_outputters::SilentFilePoseOutputter
• buffering_signals() : core::conformation::Conformation
• BufferMap : protocols::jd2::SingleFileBuffer
• Buffers : protocols::jd2::MpiFileBuffer
• build() : core::chemical::AtomICoor , core::chemical::MutableICoorRecord , 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_all_loops_ : protocols::loops::loop_mover::IndependentLoopMover
• 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_attempts_ : protocols::loops::loop_mover::IndependentLoopMover
• build_backbone_rotamer_clouds() : protocols::simple_moves::ExplicitWaterMover
• 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_coords_for_clash_checking_ : protocols::match::downstream::TargetRotamerCoords
• 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_Dmtrx() : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• 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_geometry_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• 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::ExplicitWaterMover
• 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_overlap_ : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• 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_positionOPs_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• build_pwat_rotamers() : core::pack::rotamer_set::RotamerSubset
• build_query_loops_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• 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_ : 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_round1_hits_twice_ : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::Matcher , 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_set_id_for_restype_ : protocols::match::Matcher
• build_sets_ : protocols::match::upstream::ProteinUpstreamBuilder
• build_sidechain_rotamers() : protocols::jumping::ResiduePairJump
• build_site_only_ : protocols::sewing::movers::LigandBindingAssemblyMover
• build_stage() : protocols::loop_modeler::LoopModeler
• 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
• build_xyz() : core::chemical::MutableICoorRecord
• buildable() : core::chemical::ICoorAtomID , core::chemical::MutableICoorRecord
• buildAdjacentLists() : protocols::cluster::calibur::Clustering
• BuildAlaPose() : protocols::protein_interface_design::movers::BuildAlaPose
• buildboundary() : core::scoring::atomic_depth::AtomicDepth
• BuildDeNovoBackboneMover() : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• buildDisulfide : protocols::forge::remodel::RemodelWorkingSet
• builder_ : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• builder_loop() : protocols::jumping::SheetBuilder
• builders() : core::scoring::lkball::WaterBuilderForRestype
• builders_ : core::scoring::lkball::WaterBuilderForRestype
• BuildingBlockInterfaceOperation() : protocols::matdes::BuildingBlockInterfaceOperation
• BuildInstruction() : protocols::forge::build::BuildInstruction
• BuildInstructionCAPs : protocols::forge::build::BuildInstruction
• BuildInstructionOP : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• BuildInstructionOPs : protocols::forge::build::BuildManager
• BuildManager : protocols::fldsgn::BluePrintBDR , protocols::forge::build::BuildManager , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover
• 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
• buildtype_ : protocols::parser::BluePrint
• built_atom() : core::chemical::AtomICoor
• built_atom_ : core::chemical::AtomICoor
• bulge_apply_mover_ : protocols::stepwise::screener::BulgeApplier
• bulge_at_chain_closure_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• bulge_bonus_ : core::scoring::rna::RNA_BulgeEnergy
• 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_res : protocols::stepwise::modeler::rna::sugar::SugarModeling
• bulge_res_ : core::import_pose::FullModelPoseBuilder , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• bulge_res_base_state : protocols::stepwise::modeler::rna::sugar::SugarModeling
• bulge_res_pucker_state : protocols::stepwise::modeler::rna::sugar::SugarModeling
• bulge_suite : protocols::stepwise::modeler::rna::sugar::SugarModeling
• bulge_unapply_mover_ : protocols::stepwise::screener::BulgeApplier
• bulge_variant_decision() : protocols::stepwise::screener::BulgeApplier
• BulgeApplier() : protocols::stepwise::screener::BulgeApplier
• BulgeApplyMover() : protocols::stepwise::modeler::rna::bulge::BulgeApplyMover
• bulges1_ : protocols::fldsgn::topology::StrandPairing
• bulges2_ : protocols::fldsgn::topology::StrandPairing
• bulges_ : protocols::denovo_design::architects::StrandArchitect
• 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_ : core::pack::task::PackerTask_ , protocols::minimization_packing::BoltzmannRotamerMover , protocols::motifs::MotifSearch , protocols::simple_moves::CoupledMover
• bump_check_backbone() : core::scoring::ScoreFunction
• bump_check_full() : core::scoring::ScoreFunction
• bump_cutoff_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• BUMP_ENERGY : core::scoring::nmr::NMRSpinlabel
• 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_grid_ : protocols::match::output::MatchCollisionFilter
• bump_overlap_factor_ : core::pack::task::residue_selector::ClashBasedShellSelector , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• bump_parameter() : core::scoring::rna::RNA_AtomVDW
• bump_parameter_rnp() : core::scoring::rna::RNA_AtomVDW
• bump_selector_ : core::pack::rotamer_set::RotamerSet_ , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• bump_threshold_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• BumpGrid() : protocols::match::BumpGrid
• BumpSelector() : core::pack::rotamer_set::BumpSelector
• bundle_calculator() : protocols::helical_bundle_predict::HBPHelixParameters
• bundle_calculator_ : protocols::helical_bundle_predict::HBPHelixParameters
• bundle_symmetry() : protocols::helical_bundle::parameters::BundleParametersSet
• bundle_symmetry_ : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::parameters::BundleParametersSet
• bundle_symmetry_copies() : protocols::helical_bundle::parameters::BundleParametersSet
• bundle_symmetry_copies_ : protocols::helical_bundle::MakeBundle , protocols::helical_bundle::parameters::BundleParametersSet
• BundleGridSampler() : protocols::helical_bundle::BundleGridSampler
• BundleGridSamplerHelper() : protocols::helical_bundle::BundleGridSamplerHelper
• BundleParameters : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• BundleParametersCOP : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• BundleParametersOP : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• BundleParametersSet : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• bundleparametersset_index() : protocols::helical_bundle::PerturbBundle
• bundleparametersset_index_ : protocols::helical_bundle::PerturbBundle
• BundleParametersSetCOP : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• BundleParametersSetOP : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• BundleParametrizationCalculator() : protocols::helical_bundle::BundleParametrizationCalculator
• BundleReporterFilter() : protocols::helical_bundle::BundleReporterFilter
• bunsat_edge_pool_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph
• bur_dist_ : protocols::pockets::PocketGrid
• bur_score_ : protocols::pockets::PocketGrid
• burial() : core::scoring::motif::Xfrag
• burial_ : core::scoring::motif::Xfrag , core::select::util::SelectResiduesByLayer
• burial_atomic_depth_ : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty
• burial_cutoff_ : protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::switches::GraftSwitchMover
• burial_cutoff_apo_ : protocols::simple_filters::BuriedUnsatHbondFilter
• burial_deriv() : core::scoring::elec::FA_GrpElecEnergy
• burial_function_ : core::scoring::rna::data::RNA_DataBackboneEnergy
• burial_probe_radius_ : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty
• burial_resolution_ : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty
• burial_sigmoid() : core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy
• burial_threshold() : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions
• 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
• burialWt_ : protocols::simple_moves::StructProfileMover
• buried : core::scoring::sc::_DOT , core::scoring::sc::Atom
• 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::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfacePotential
• buried_unsatisfied_penalty_burial_threshold() : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_burial_threshold_ : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_cone_angle_exponent() : 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_angle_shift_factor_ : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_cone_dist_exponent() : 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_cone_dist_midpoint_ : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_hbond_energy_threshold() : core::scoring::methods::EnergyMethodOptions
• buried_unsatisfied_penalty_hbond_energy_threshold_ : core::scoring::methods::EnergyMethodOptions
• BuriedSurfaceAreaFilter() : protocols::simple_filters::BuriedSurfaceAreaFilter
• BuriedUnsatHbondFilter() : protocols::simple_filters::BuriedUnsatHbondFilter
• BuriedUnsatisfiedPolars_ : protocols::analysis::InterfaceAnalyzerMover
• 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
• burunsat_atoms_ : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• bUseInputPose_ : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::StartStructClaimer
• bUseJobPose_ : protocols::topology_broker::TopologyBroker
• bUseThreadingJobLoops_ : protocols::topology_broker::RigidChunkClaimer
• bUseXYZ_in_cstfile_ : protocols::topology_broker::CoordConstraintClaimer
• bValidTree_ : protocols::jumping::JumpSample
• bw_sfxn_ : protocols::hbnet::HBNet
• bWriteIntermediateFiles_ : protocols::jd2::RNA_DeNovoJobOutputter , protocols::jd2::SilentFileJobOutputter
• bWriteIntermediateStructures_ : protocols::jd2::RNA_DeNovoJobOutputter , protocols::jd2::SilentFileJobOutputter
• bWriteNoStructures_ : protocols::jd2::RNA_DeNovoJobOutputter , protocols::jd2::SilentFileJobOutputter
• bX_ : core::grid::CartGrid< T >
• bx_init() : core::optimization::MinimizerOptions
• bx_init_ : core::optimization::MinimizerOptions
• bY_ : core::grid::CartGrid< T >
• by_aln() : protocols::protein_interface_design::filters::RmsdFilter
• by_aln_ : protocols::protein_interface_design::filters::RmsdFilter
• by_helices_ : protocols::simple_filters::HelixHelixAngleFilter
• by_resid_ : protocols::noesy_assign::ResonanceList
• by_string_ : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Translate_info
• bYieldCutBias_ : protocols::abinitio::abscript::FragmentCM
• byte_index_from_doublebin() : protocols::match::Bool3DGrid
• bytes_ : protocols::moves::UDPSocketClient::UUID
• bZ_ : core::grid::CartGrid< T >