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

- b -

• b : protocols::md::Constraint , protocols::pockets::UnionEdge , protocols::sic_dock::Vec3
• 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_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_ : 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_allow_independent_alignment_per_fragment : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• b_ang_ : protocols::coarse_rna::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::CORdata
• 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::coarse_rna::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_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::loophash::LegacyLeapIndex
• bab_motif() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• bab_motifs() : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• bab_motifs_ : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• backbone_ : protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::simple_filters::AtomicContactFilter
• backbone_database() : protocols::loophash::LoopHashLibrary
• backbone_for_moltenres_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_for_resid_bbconf() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• backbone_index_map_ : protocols::loophash::LoopHashMap
• backbone_only() : protocols::match::upstream::BuildSet
• backbone_only_ : protocols::forge::remodel::RemodelEnzdesCstModule , protocols::match::upstream::BuildSet , protocols::simple_moves::CopyDofMover , protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• 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
• BackboneSampler() : protocols::enzdes::BackboneSampler
• BackboneSegment() : protocols::loophash::BackboneSegment
• BackboneTorsionPerturbation() : protocols::hybridization::BackboneTorsionPerturbation
• BackboneTorsionSampler() : protocols::hybridization::BackboneTorsionSampler
• background_energies_ : protocols::pack_daemon::PackDaemon
• backrub() : protocols::dna::DesignProteinBackboneAroundDNA
• backrub_ : protocols::enzdes::EnzRepackMinimize , protocols::forge::remodel::RemodelMover::instruction_flags
• backrub_move() : protocols::flexpep_docking::FlexPepDockingProtocol
• backrub_mover_ : protocols::backrub::BackrubSidechainMover
• backrub_moves_ : protocols::protein_interface_design::movers::BackrubDDMover
• backrub_opt : protocols::flexpep_docking::FlexPepDockingFlags
• backrub_partner1_ : protocols::protein_interface_design::movers::BackrubDDMover
• backrub_partner2_ : protocols::protein_interface_design::movers::BackrubDDMover
• BackrubDDMover() : protocols::protein_interface_design::movers::BackrubDDMover
• BackrubMover() : protocols::backrub::BackrubMover
• backrubmover_ : protocols::simple_moves::ShortBackrubMover
• BackrubSegment() : protocols::backrub::BackrubSegment
• BackrubSidechainMover() : protocols::backrub::BackrubSidechainMover
• backtrack() : protocols::coarse_rna::CoarseRNA_LoopCloser
• backward_check() : protocols::motifs::Motif
• backward_jump() : protocols::motifs::Motif
• backward_jump_ : protocols::motifs::Motif
• backward_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• backward_threshold_ : protocols::simple_moves::WobbleMover
• bad : protocols::jd2::archive::MPIArchiveJobDistributor::CompletionMessage , protocols::jd2::InnerJob , protocols::jd2::Job
• bad_ : protocols::jd2::InnerJob
• bad_input_jobs_ : protocols::jd2::MPIFileBufJobDistributor
• bad_job_id_ : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• BAD_LOW_PROB : protocols::noesy_assign::CrossPeak
• bad_nter_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::ModelCDRH3
• BAD_SCORE : protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase
• BalancedKicMover() : protocols::kinematic_closure::BalancedKicMover
• bAlign_ : protocols::topology_broker::FibrilModelingClaimer
• bAllowAdjacentJumps_ : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• bAllowPureMovers_ : protocols::environment::Environment
• 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
• bApplyEndBias_ : protocols::simple_moves::ClassicFragmentMover
• barcode_extend_stems() : protocols::LoopRebuild
• barrier() : protocols::optimize_weights::IterativeOptEDriver , protocols::pmut_scan::PointMutScanDriver
• base() : protocols::dna::DNAParameters
• Base : protocols::jd2::WriteFileSFB
• base_ : protocols::antibody_legacy::CDRH3Modeler
• 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_bin_map_ : protocols::stepwise::screener::BaseBinMapUpdater
• base_centroid_checker_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::BulgeApplier
• base_only() : protocols::dna::RestrictDesignToProteinDNAInterface
• base_only_ : protocols::dna::DnaInterfaceFinder , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::RotamerDNAHBondFilter
• base_pair_axis_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pair_dist_max_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pair_dist_min_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• 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_step_ : protocols::farna::BasePairStep
• base_pair_step_library_ : protocols::farna::RNA_ChunkLibrary
• base_pair_step_sequence_ : protocols::farna::BasePairStepSequence
• base_pair_z_offset_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_pairing_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• 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_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_planarity_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• 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_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_stub_list_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• base_weight() : protocols::topology_broker::weights::ConstAbinitioMoverWeight
• 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
• basehalfbin_ : protocols::match::VoxelSetIterator
• BaseJobDistributor() : protocols::jobdist::BaseJobDistributor
• baseline() : protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter
• baseline_ : protocols::simple_filters::DeltaFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::Sigmoid
• baseline_checkpointing_filename() : protocols::simple_filters::Sigmoid
• baseline_checkpointing_filename_ : protocols::simple_filters::Sigmoid
• baseline_val() : protocols::simple_filters::RelativePoseFilter
• baseline_val_ : protocols::simple_filters::RelativePoseFilter
• basepair() : protocols::dna::DNAParameters
• basepairs_ : protocols::dna::DNAParameters
• basepairs_begin() : protocols::dna::DNAParameters
• basepairs_end() : protocols::dna::DNAParameters
• BasePairStep() : protocols::farna::BasePairStep
• BasePairStepLibrary() : protocols::farna::BasePairStepLibrary
• BasePairStepSequence() : protocols::farna::BasePairStepSequence
• BasePairType() : protocols::farna::BasePairType
• bases_ : protocols::dna::DNAParameters
• bases_begin() : protocols::dna::DNAParameters
• bases_end() : protocols::dna::DNAParameters
• 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_design_ : protocols::antibody::design::AntibodySeqDesignMover , protocols::antibody::design::AntibodySeqDesignTFCreator
• basic_init_ : protocols::rpc::JSON_RPC
• BasicCDRClusterSet() : protocols::antibody::clusters::BasicCDRClusterSet
• BasicCmdLineInit() : protocols::rpc::BasicCmdLineInit
• BasicInit() : protocols::rpc::BasicInit
• BasicJob() : protocols::jobdist::BasicJob
• BasicJumpClaimer() : protocols::topology_broker::BasicJumpClaimer
• BasicSimAnnealerRepacker() : protocols::pack_daemon::BasicSimAnnealerRepacker
• batch() : protocols::jd2::archive::Batch
• Batch() : protocols::jd2::archive::Batch
• batch() : protocols::jd2::JobDistributor
• batch_apply() : protocols::relax::FastRelax
• batch_description_ : protocols::features::ReportToDB
• batch_features_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• 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() : 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::dna::DnaInterfaceMinMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::TaskAwareMinMover
• 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::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::RepGrid , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::TaskAwareMinMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes
• bb_backrub_ : protocols::enzdes::EnzdesBaseProtocol
• bb_bb() : 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_bins_from_pose() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• bb_clashes_ : protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• bb_dihedral_tolerance_ : protocols::fldsgn::SheetConstraintsRCG
• bb_extended_ : protocols::match::Bool3DGrid
• bb_grid_ : protocols::match::downstream::DownstreamBuilder , protocols::match::Matcher
• bb_hbond_ : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• bb_ids_ : protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::MakeRotLibOptionsData , protocols::make_rot_lib::RotData
• bb_interface_builder_ : protocols::ligand_docking::MoveMapBuilder
• bb_interface_cutoff_ : protocols::ligand_docking::LigandBaseProtocol
• bb_min_ : protocols::enzdes::EnzdesBaseProtocol
• bb_min_allowed_dev_ : protocols::enzdes::EnzdesBaseProtocol
• bb_moves_ : protocols::enzdes::BackboneSampler
• bb_only() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• bb_only_ : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• BB_Pos : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::SS_Base
• bb_pos() : protocols::fldsgn::topology::SS_Info2
• BB_Pos : protocols::fldsgn::topology::SS_Info2
• bb_pos_ : protocols::fldsgn::topology::SS_Info2
• bb_precision_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• bb_ranges_ : protocols::make_rot_lib::MakeRotLibOptionsData
• bb_rotamer_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• bb_samplers_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• 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
• BBdisplay_state : protocols::viewer::GraphicsState
• 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
• bbindices_up_to_date() : protocols::fldsgn::topology::BB_Pos
• bbl_ : protocols::scoring::ImplicitFastClashCheck
• bbl_ca_ : protocols::scoring::ImplicitFastClashCheck
• bblock_dist_ : protocols::matdes::BuildingBlockInterfaceOperation
• bbM1 : protocols::abinitio::abscript::AtomPack
• bbmove_ : protocols::hybridization::CartesianSampler
• 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() : protocols::frag_picker::VallResidue
• BBTorsionSRFD : protocols::frag_picker::VallResidue
• BBTorsionSRFDOP : 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
• 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
• be_lenient() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• be_lenient_ : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• before_chain_break_grid_index_screening : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• before_minimization_reference_energies_ : protocols::optimize_weights::IterativeOptEDriver
• begin() : protocols::abinitio::abscript::ResidueChunkSelection , protocols::abinitio::PairingStatistics , protocols::abinitio::Templates , protocols::dna::DnaChains , protocols::filters::CompoundFilter , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::StrandPairingSet , protocols::forge::build::BuildManager , protocols::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::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::TryRotamers , protocols::rosetta_scripts::ParsedProtocol , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::topology_broker::TopologyBroker , protocols::wum::SilentStructStore , protocols::wum::WorkUnitQueue
• begin1() : protocols::fldsgn::topology::StrandPairing
• begin1_ : protocols::fldsgn::topology::StrandPairing
• begin2() : protocols::fldsgn::topology::StrandPairing
• begin2_ : protocols::fldsgn::topology::StrandPairing
• begin_ : protocols::fldsgn::topology::SS_Base , protocols::jd2::parser::FragmentReader , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• begin_chain_pair() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• begin_critical_section() : protocols::jd2::BOINCJobDistributor , protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor
• begin_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_stage() : protocols::abinitio::abscript::AbscriptMover::StageTracker
• begin_structure() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• behavior_non_catalytic_ : protocols::enzdes::SetCatalyticResPackBehavior
• bEnableCcdMoves_ : protocols::loops::loop_closure::ccd::LoopClosure
• benchmark_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::CloseOneCDRLoop , protocols::antibody::design::AntibodyGraftDesignMover , 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::ModelCDRH3 , protocols::antibody::RefineOneCDRLoop , protocols::antibody::RefineOneCDRLoopCentroid , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::CloseOneMover , protocols::antibody_legacy::GraftMover , protocols::antibody_legacy::GraftOneMover , protocols::antibody_legacy::LoopRlxMover
• bend() : protocols::fldsgn::topology::Helix
• bend_ : protocols::fldsgn::topology::Helix
• bend_angle_ : protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• bEnumeratedLastTime_ : protocols::abinitio::IterativeBase
• Berendsen_Integrator() : protocols::md::CartesianMD
• best_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• best_address_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• best_assignment() : protocols::pack_daemon::PackDaemon
• best_assignment_ : protocols::pack_daemon::PackDaemon
• best_assignment_valid_ : protocols::pack_daemon::PackDaemon
• best_by_ala_scan() : protocols::seeded_abinitio::SeedFoldTree
• best_candidate_rmsds_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• best_combine_score_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• best_cyclic_peptides_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• 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_fitness_ : protocols::multistate_design::MultiStateFitnessFunction
• best_fitness_from_current_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• best_fragment_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• best_Kmer_rms() : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• best_linear_peptides_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• best_match_dspos1s_ : protocols::match::output::BestMatchesCollection
• best_matches_ : protocols::match::output::BestMatchesCollection
• best_motifhits() : protocols::motifs::BuildPosition
• best_motifhits_ : protocols::motifs::BuildPosition
• best_motifs() : protocols::motifs::BuildPosition
• best_motifs_ : protocols::motifs::BuildPosition
• best_packscore_ : protocols::flxbb::FilterStructs_Packstat
• best_pose_ : protocols::flxbb::FilterStructs
• best_rotamers() : protocols::motifs::BuildPosition
• best_rotamers_ : protocols::motifs::BuildPosition
• best_score() : protocols::multistate_design::SingleState , protocols::relax::SRelaxPose
• best_score_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure , protocols::multistate_design::SingleState
• best_score_log : protocols::relax::SRelaxPose
• best_struct : protocols::relax::SRelaxPose
• BestHotspotCstMover() : protocols::protein_interface_design::movers::BestHotspotCstMover
• BestMatchesCollection() : protocols::match::output::BestMatchesCollection
• BestTotalScoreSelector() : protocols::frag_picker::BestTotalScoreSelector
• beta() : protocols::dna::DNABase , protocols::protein_interface_design::Transformation , protocols::stepwise::sampler::rigid_body::EulerAngles , Transformation
• beta_ : protocols::dna::DNABase , protocols::simple_filters::AbinitioBaseFilter , protocols::stepwise::sampler::rigid_body::EulerAngles
• beta_id_i_ : protocols::features::strand_assembly::StrandFragment
• beta_id_j_ : protocols::features::strand_assembly::StrandFragment
• 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
• BetaTurnDetection() : protocols::features::BetaTurnDetection
• BetaTurnDetectionFeatures() : protocols::features::BetaTurnDetectionFeatures
• BetaTurnDetectionFeaturesCreator() : protocols::features::BetaTurnDetectionFeaturesCreator
• bExclusive_ : protocols::topology_broker::RigidChunkClaimer
• bF() : protocols::frag_picker::VallResidue
• bF_ : protocols::frag_picker::VallResidue
• BFactor() : protocols::frag_picker::scores::BFactor
• bfactor_ : protocols::simple_moves::DumpPdb
• 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
• bGDT_ : protocols::simple_filters::RmsdEvaluator
• 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::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• 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_frag_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• bigbin() : protocols::frags::VallData
• bigbin_ : protocols::frags::VallData
• bIgnoreSequenceSeparation() : protocols::abinitio::FoldConstraints
• bIgnoreSequenceSeparation_ : protocols::abinitio::FoldConstraints
• bin() : protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• BIN : protocols::sic_dock::SICFast
• Bin3D : protocols::match::Bool3DGrid , protocols::match::Bool3DGridKinemageWriter , protocols::match::BumpGrid
• Bin6D : protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::VoxelSetIterator
• bin_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• bin_center() : protocols::match::Bool3DGrid
• bin_count_ : protocols::ligand_docking::ComputeLigandRDF
• bin_extrema() : protocols::match::Bool3DGrid
• bin_for_point() : protocols::match::Bool3DGrid
• bin_index_() : protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::TorsionBinSimilarity
• bin_max_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• bin_min_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• bin_names_ : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• bin_offset_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• bin_probs_ : protocols::frag_picker::quota::ABEGO_SS_Config
• bin_size_ : protocols::frag_picker::scores::AdaptiveScoreHistogram , 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_ : 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_width() : protocols::match::Bool3DGrid
• bin_width_ : protocols::match::Bool3DGrid , protocols::match::downstream::ActiveSiteGrid
• bin_width_2x_ : protocols::match::Bool3DGrid
• binary_ : protocols::outputter::SilentFileOutputter
• binary_rna_output_ : protocols::farna::RNA_DeNovoProtocol
• bind_vec_constraint() : protocols::antibody::AntibodyDatabaseManager
• binding_E_ : protocols::dna::DnaInterfacePacker
• BindingSiteConstraint() : protocols::constraints_additional::BindingSiteConstraint
• BindingSiteConstraintCreator() : protocols::constraints_additional::BindingSiteConstraintCreator
• BindingStrainFilter() : protocols::protein_interface_design::filters::BindingStrainFilter
• 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
• binner() : protocols::match::HitHasher
• binner_ : protocols::match::HitNeighborFinder , protocols::match::MatchCounter
• BIOPConstIterator : protocols::forge::build::BuildManager , protocols::forge::components::VarLengthBuild
• BIOPIterator : protocols::forge::build::BuildManager
• bitmask_for_position() : protocols::match::OccupiedSpaceHash
• bKeepFilesAlive_ : protocols::jd2::MpiFileBuffer
• bKeepFragments_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• bKeepJumpsFromInputPose_ : protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FragmentJumpClaimer
• BL1_1 : protocols::sparta::ANN
• BL1_2 : protocols::sparta::ANN
• BL1_3 : protocols::sparta::ANN
• BL2_1 : protocols::sparta::ANN
• BL2_2 : protocols::sparta::ANN
• BL2_3 : protocols::sparta::ANN
• blacklist_ : protocols::wum::WorkUnitBase
• blanket_assign_state_0() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• bLocal_ : protocols::topology_broker::CoordConstraintClaimer
• block() : protocols::jd2::SingleFileBuffer , protocols::jd2::WriteFileSFB
• block_file() : protocols::jd2::MpiFileBuffer
• blocked_files_ : protocols::jd2::MpiFileBuffer
• BLOSUM_62 : protocols::sparta::Sparta::SpartaLib
• 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::jd2::parser::BluePrint , protocols::toolbox::task_operations::DsspDesignOperation
• blueprint_ : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintsRCG , protocols::flxbb::FlxbbDesign , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelMover , protocols::jd2::parser::FragmentReader , protocols::toolbox::task_operations::DsspDesignOperation
• blueprint_cst_definition() : protocols::forge::remodel::RemodelEnzdesCstModule
• BluePrintBDR() : protocols::fldsgn::BluePrintBDR
• BluePrintOP : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintsRCG , protocols::flxbb::FlxbbDesign , protocols::toolbox::task_operations::DsspDesignOperation
• bMinTrial_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• bNoRecoverLowAtSwitch_ : protocols::abinitio::ConstraintFragmentSampler
• BOGUS_ASSIGNMENTS : protocols::noesy_assign::PeakAssignmentResidueMap
• BOGUS_BATCH_ID : protocols::jd2::BatchJobInputter
• Boinc() : protocols::boinc::Boinc
• boinc_mode_ : protocols::canonical_sampling::CanonicalSamplingMover
• BoincCurrentPoseObserver() : protocols::boinc::BoincCurrentPoseObserver
• BOINCJobDistributor() : protocols::jd2::BOINCJobDistributor
• boltz_rank() : protocols::simple_moves::GenericMonteCarloMover
• boltz_rank_ : protocols::simple_moves::GenericMonteCarloMover
• boltz_temp_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• boltzmann() : protocols::canonical_sampling::BiasedMonteCarlo , protocols::moves::DualMonteCarlo , protocols::moves::MonteCarlo , protocols::moves::ReplicaExchangeMC , protocols::moves::SimulatedTempering , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::TorsionDOFMover
• boltzmann_kbt_ : protocols::generalized_kinematic_closure::selector::GeneralizedKICselector
• boltzmann_rotamer_mover_ : protocols::simple_moves::CoupledMover
• BoltzmannFilter() : protocols::protein_interface_design::filters::BoltzmannFilter
• BoltzmannRotamerMover() : protocols::simple_moves::BoltzmannRotamerMover
• bond_angle_atoms() : protocols::backrub::BackrubSegment
• bond_angle_map_ : protocols::backrub::BackrubMover
• bond_angle_residue_type_param_set() : protocols::branch_angle::BranchAngleOptimizer
• bond_angle_residue_type_param_set_ : 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_length() : protocols::simple_moves::CutChainMover
• bond_length_ : protocols::simple_moves::CutChainMover
• bond_length_sd_ : protocols::simple_moves::ConstrainToIdealMover
• bond_length_sd_polar_hydrogen_ : protocols::simple_moves::ConstrainToIdealMover
• bond_lengths_ : protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::perturbers::LogFilePerturber
• bond_torsion_sd_ : protocols::simple_moves::ConstrainToIdealMover
• bond_torsion_sd_polar_hydrogen_ : protocols::simple_moves::ConstrainToIdealMover
• BondAngleKey : protocols::backrub::BackrubSegment
• bondlen_precision_ : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor
• bondlist : protocols::cartesian::MolecularDynamics
• bonds_scorefxn_ : protocols::seeded_abinitio::SegmentHybridizer
• bonus_ : protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle
• bonus_value() : protocols::hotspot_hashing::HotspotStub
• bonus_value_ : protocols::hotspot_hashing::HotspotStub
• Bool3DGrid() : protocols::match::Bool3DGrid
• Bool3DGridKinemageWriter() : protocols::match::Bool3DGridKinemageWriter
• BoolDataCacheBoolOP : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• 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
• both_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• both_criteria_needed_to_pass_ : protocols::match::NumNeighborsMPM
• BOTH_SC_AND_BB : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• bottom() : protocols::dna::DnaPosition
• bottom_ : protocols::dna::DnaPosition
• bound() : protocols::simple_filters::NonSequentialNeighborsFilter
• bound_ : protocols::optimize_weights::DGBindOptEData , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::toolbox::task_operations::ProteinCore
• bound_energies_ : protocols::simple_moves::ddG
• bound_per_residue_energies_ : protocols::simple_moves::ddG
• bound_struct() : protocols::optimize_weights::DGBindOptEData
• bound_total_energy_ : protocols::simple_moves::ddG
• bound_width() : protocols::simple_moves::AddConstraintsToCurrentConformationMover
• bound_width_ : protocols::electron_density::DensityMorphingMover , protocols::simple_moves::AddConstraintsToCurrentConformationMover
• boundary_ : protocols::toolbox::task_operations::SelectBySASAOperation
• bounded() : protocols::relax::AtomCoordinateCstMover
• bounded_ : protocols::relax::AtomCoordinateCstMover
• bounded_protocol() : protocols::frag_picker::FragmentPicker
• BoundedCollector() : protocols::frag_picker::BoundedCollector< StrictWeakOrdering >
• BoundedCollector_CompareTotalScore() : protocols::frag_picker::BoundedCollector_CompareTotalScore
• BoundedCollectorCOP : protocols::frag_picker::BoundedCollector< StrictWeakOrdering >
• BoundedCollectorOP : protocols::frag_picker::BoundedCollector< StrictWeakOrdering >
• bounding_box() : protocols::match::downstream::ActiveSiteGrid
• bounding_radius_for_rotamers() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• bounding_volumes_for_bb_for_aa_ : protocols::flexpack::interaction_graph::OTFFlexbbNode
• BoundingBox : protocols::match::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
• 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
• bp_motifhits() : protocols::motifs::MotifSearch
• bp_rotamers() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• bpdata_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• bpdata_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• bps_moves_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_StructureParameters
• 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
• bRampChainbreak_ : protocols::loops::loop_closure::ccd::LoopClosure
• bRampChainbreaks_ : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::KinematicAbinitio
• bRampCoordConstraints_ : protocols::abinitio::ConstraintFragmentSampler
• BranchAngleOptimizer() : protocols::branch_angle::BranchAngleOptimizer
• BranchCoef1() : protocols::branch_angle::BranchCoef1
• BranchCoef2() : protocols::branch_angle::BranchCoef2
• branchopt() : protocols::backrub::BackrubMover
• branchopt_ : protocols::backrub::BackrubMover
• BranchParam1() : protocols::branch_angle::BranchParam1
• BranchParam2() : protocols::branch_angle::BranchParam2
• bRandomSheet_ : protocols::topology_broker::TemplateJumpClaimer
• bRegenerateFromInputPose_ : protocols::topology_broker::CoordConstraintClaimer
• bRelative_ : protocols::environment::claims::XYZClaim
• bRelax_ : protocols::abinitio::AbrelaxApplication
• Bridge() : protocols::forge::build::Bridge
• bridge_res() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• bridge_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• bRigidInRelax_ : protocols::topology_broker::RigidChunkClaimer
• broadcast_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• broadcast_entity_string() : protocols::pack_daemon::MPIMultistateFitnessFunction
• broadcast_newest_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• broker() : protocols::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
• 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
• buckle() : protocols::dna::DNABasepair
• buckle_ : protocols::dna::DNABasepair
• buf : protocols::sparta::ANN , protocols::sparta::GDB , protocols::sparta::Sparta::SpartaLib
• buf_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• buf_to_address() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• buffer_factor_ : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• buffer_length_ : protocols::simple_moves::WobbleMover
• buffer_rank_ : protocols::jd2::MpiFileBuffer
• BufferMap : protocols::jd2::SingleFileBuffer
• Buffers : protocols::jd2::MpiFileBuffer
• build() : protocols::ligand_docking::InterfaceBuilder , protocols::ligand_docking::MoveMapBuilder , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder
• build_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_attempts_ : protocols::loops::loop_mover::IndependentLoopMover
• 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() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dangle_seq1_5prime() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dangle_seq2_3prime() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dangle_seq2_5prime() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dangling_ends() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_dependent_rotamers() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• build_design_taskset() : protocols::flxbb::FlxbbDesign
• build_fold_tree() : protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyBroker , protocols::topology_broker::TopologyClaimer
• build_fold_tree_from_claimer() : protocols::topology_broker::TopologyBroker
• build_from_three_coords() : protocols::match::downstream::ClassicMatchAlgorithm
• build_full_model() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• build_fullatom_loop() : protocols::antibody_legacy::CDRH3Modeler
• build_helix() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_hits_at_all_positions() : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• build_ideal_geometry_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• build_init_pose() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_inverted_rotamers() : protocols::motifs::Motif
• build_loop_with_ccd_closure() : protocols::LoopRebuild
• build_loops() : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• build_mover() : protocols::loops::loop_mover::LoopCM
• build_new_residues() : protocols::environment::EnvClaimBroker
• build_on_base_pair() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• build_pair_dis_matrix() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• build_point() : protocols::match::Matcher
• build_positionOPs() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• build_positionOPs_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• build_query_loops_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingMover
• build_random_loops() : protocols::LoopRebuild
• build_receptor_peptide_pose() : protocols::analysis::PeptideDeriverFilter
• build_residue_vector_from_fragment() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• build_rotamer() : protocols::motifs::MotifHit
• build_rotamer_ : protocols::motifs::MotifHit
• build_rotamer_list() : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• build_rotamers() : protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::motifs::Motif
• build_rotamers_for_concrete_virt() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• build_round1_hits_twice() : protocols::match::MatcherTask
• build_round1_hits_twice_ : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::Matcher , protocols::match::MatcherTask
• 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_stage() : protocols::loop_modeling::LoopModeler
• build_stage_ : protocols::loop_modeling::LoopModeler
• build_structures() : protocols::loophash::LoopHashSampler
• build_temperature_list() : protocols::moves::ReplicaExchangeMC
• BuildAlaPose() : protocols::protein_interface_design::movers::BuildAlaPose
• buildDisulfide : protocols::forge::remodel::RemodelWorkingSet
• builder_loop() : protocols::jumping::SheetBuilder
• 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
• BuildPosition() : protocols::motifs::BuildPosition
• BuildPosition_from_Size() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• BuildSet() : protocols::match::upstream::BuildSet
• buildtype() : protocols::jd2::parser::BluePrint
• buildtype_ : protocols::jd2::parser::BluePrint
• bulge_apply_mover_ : protocols::stepwise::screener::BulgeApplier
• bulge_at_chain_closure_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• 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_res : protocols::stepwise::modeler::rna::sugar::SugarModeling
• bulge_res_ : 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
• BulgeUnApplyMover() : protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover
• bump_check() : protocols::flexpack::rotamer_set::FlexbbRotamerSet
• bump_check_ : protocols::motifs::MotifSearch , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover
• bump_cutoff_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• bump_grid() : protocols::match::output::MatchCollisionFilter
• bump_grid_ : protocols::match::output::MatchCollisionFilter
• bump_overlap_factor_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• bump_selector_ : protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• bump_threshold_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• BumpGrid() : protocols::match::BumpGrid
• bundle_parameters() : protocols::helical_bundle::MakeBundleHelix
• bundle_parameters_ : protocols::helical_bundle::MakeBundleHelix
• bundle_size_ : protocols::features::helixAssembly::HelixBundleFeatures
• 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
• bUpdateMM_ : protocols::abinitio::abscript::AbscriptLoopCloserCM
• bur_dist_ : protocols::pockets::PocketGrid
• bur_score_ : protocols::pockets::PocketGrid
• burial_ : protocols::toolbox::SelectResiduesByLayer
• burial_sasa_cutoff_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• BuriedPolarScore() : protocols::sic_dock::BuriedPolarScore
• BuriedUnsatHbondFilter() : protocols::simple_filters::BuriedUnsatHbondFilter
• BuriedUnsatisfiedPolars_ : protocols::analysis::InterfaceAnalyzerMover
• BuriedUnsatisfiedPolarsCalculator() : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• burunsat_atoms() : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• burunsat_atoms_ : protocols::toolbox::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
• bWriteIntermediateFiles_ : protocols::jd2::SilentFileJobOutputter
• bWriteIntermediateStructures_ : protocols::jd2::SilentFileJobOutputter
• bWriteNoStructures_ : protocols::jd2::SilentFileJobOutputter
• by_aln() : protocols::protein_interface_design::filters::RmsdFilter
• by_aln_ : protocols::protein_interface_design::filters::RmsdFilter
• by_resid_ : protocols::noesy_assign::ResonanceList
• bYieldCutBias_ : protocols::abinitio::abscript::FragmentCM
• byte_index_from_doublebin() : protocols::match::Bool3DGrid
• bytes_ : protocols::moves::UDPSocketClient::UUID