- a -

• a : core::scoring::packstat::PointPair , protocols::md::Constraint , protocols::pockets::UnionEdge , protocols::sic_dock::Vec3
• a0_ : core::scoring::FACTSRsdTypeInfo
• a1_ : core::scoring::FACTSRsdTypeInfo
• a2_ : core::scoring::FACTSRsdTypeInfo
• a3_ : core::scoring::FACTSRsdTypeInfo
• A_ : core::io::CrystInfo
• a_ : core::scoring::carbohydrates::CHIEnergyFunction , core::scoring::electron_density::KromerMann , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::fiber_diffraction::KromerMann
• A_ : core::scoring::func::KarplusFunc
• a_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• A_ : protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• a_ : 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
• A_all_ : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• a_axis_ : protocols::docking::EllipsoidalRandomizationMover
• A_bins : core::scoring::dna::DirectReadoutPotential
• a_form_range_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• a_form_torsions_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• a_ids_ : core::scoring::saxs::SAXSEnergy , protocols::scoring::methods::saxs::PDDFEnergy
• a_ik : protocols::cluster::Exemplar
• A_index_ : protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• a_kappa : core::scoring::disulfides::FullatomDisulfideParams13
• a_kk : protocols::cluster::DataPoint
• a_little_verbose_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• a_logA : core::scoring::disulfides::FullatomDisulfideParams13
• a_mu : core::scoring::disulfides::FullatomDisulfideParams13
• a_to_i_ : protocols::normalmode::NormalMode
• aa : protocols::forge::remodel::RemodelWorkingSet
• aa1 : protocols::farna::libraries::BasePairType
• aa1_ : core::scoring::motif::ResPairMotif
• AA1name : core::scoring::constraints::ResidueTypeLinkingConstraint
• aa2 : protocols::farna::libraries::BasePairType
• aa2_ : core::scoring::motif::ResPairMotif
• AA2name : core::scoring::constraints::ResidueTypeLinkingConstraint
• aa_ : core::chemical::ResidueType , core::chemical::ResidueTypeFinder , core::chemical::rotamers::CenrotRotamerLibrarySpecification , core::chemical::rotamers::DunbrackRotamerLibrarySpecification , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::VallResidue , core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamer_set::WaterAnchorInfo , core::pack::rotamers::SingleResiduePeptoidLibrary , core::scoring::motif::Xfres , protocols::forge::build::Bridge , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::frag_picker::VallResidue , protocols::jd2::parser::FragmentReader , protocols::noesy_assign::MethylNames , protocols::noesy_assign::Resonance , protocols::optimize_weights::PNatRotOptEPositionData
• AA_ : protocols::protein_interface_design::movers::BuildAlaPose
• aa_ : protocols::simple_moves::MakePolyXMover
• aa_block_for_baserotamer_ : core::pack::rotamer_set::ContinuousRotamerSet
• aa_block_for_samplingrotamer_ : core::pack::rotamer_set::ContinuousRotamerSet
• aa_comp_setup_ : core::scoring::aa_composition_energy::AACompositionConstraint
• aa_composition_setup_files_ : core::scoring::methods::EnergyMethodOptions
• aa_encoder_ : core::scoring::methods::NMerSVMEnergy
• aa_exp_ : protocols::optimize_weights::IterativeOptEDriver
• aa_for_rotblock_ : core::pack::rotamer_set::ContinuousRotamerSet
• aa_freq_exp_ : protocols::optimize_weights::IterativeOptEDriver
• aa_freq_obs_ : protocols::optimize_weights::IterativeOptEDriver
• aa_libraries_ : core::pack::dunbrack::RotamerLibrary
• aa_map_ : core::chemical::ResidueTypeSetCache , protocols::frag_picker::SidechainContactDistCutoff
• AA_name3_ : protocols::simple_moves::ResidueTypeConstraintMover
• aa_neighbors_for_edges_ : core::pack::interaction_graph::LinearMemNode
• aa_obs_ : protocols::optimize_weights::IterativeOptEDriver
• aa_offsets_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• aa_offsets_for_edges_ : core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::PDNode
• AA_OMG_INDEX : core::pack::dunbrack::RotamerLibraryScratchSpace
• aa_order_ : protocols::simple_moves::StructProfileMover
• aa_order_map_ : protocols::frag_picker::scores::ProfileScoreDistWeight
• aa_penalty_ : core::fragment::picking_old::vall::eval::IdentityEval
• AA_PHI_INDEX : core::pack::dunbrack::RotamerLibraryScratchSpace
• AA_PSI_INDEX : core::pack::dunbrack::RotamerLibraryScratchSpace
• aa_seq_weights_ : core::scoring::methods::SequenceDependentRefEnergy
• aa_sets_dec_line_ : protocols::pack_daemon::EntityFunc
• aa_sets_name_map_ : protocols::pack_daemon::EntityFunc
• aa_submatrix_history_list_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• aa_to_index_map_ : protocols::frag_picker::SidechainContactDistCutoff
• aa_type_ : core::pack::interaction_graph::SparseMatrixIndex
• aa_types_for_states_on_file_nodes_ : core::pack::interaction_graph::PDInteractionGraph
• aa_weights_ : core::scoring::methods::ReferenceEnergy
• AAlist : protocols::sparta::Sparta::SpartaLib
• aalist_ : core::scoring::methods::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy
• AAname : core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint
• aas_ : core::chemical::Selector_AA
• aas_at_grid : core::scoring::dna::DirectReadoutPotential
• ab_dock_chains_ : protocols::antibody::design::GeneralAntibodyModeler
• ab_fold_tree_ : protocols::protein_interface_design::movers::SetAtomTree
• ab_info_ : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::AntibodyDatabaseManager , protocols::antibody::AntibodyFeatures , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::clusters::CDRClusterSet , protocols::antibody::constraints::CDRDihedralConstraintMover , protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignProtocol , protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::design::GeneralAntibodyModeler , protocols::antibody::design::MutateFrameworkForCluster , protocols::antibody::design::NativeAntibodySeq , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftedStemOptimizer , protocols::antibody::GraftOneCDRLoop , protocols::antibody::H3CterInsert , protocols::antibody::H3PerturbCCD , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody::RefineBetaBarrel , protocols::antibody::RefineOneCDRLoop , protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• ab_manager_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• ab_movemap : protocols::antibody_legacy::Antibody
• ab_sequence_ : protocols::antibody::AntibodyInfo
• ab_t_info_ : protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::GraftOneCDRLoop
• abase2_ : core::chemical::ResidueType
• abase2_deriv : core::scoring::hbonds::HBondDerivs
• abase2_indices_ : core::chemical::ResidueType
• abase_deriv : core::scoring::hbonds::HBondDerivs
• abego : protocols::denovo_design::connection::Connection::Motif , protocols::denovo_design::task_operations::LoopInfo , protocols::forge::remodel::RemodelData , protocols::forge::remodel::RemodelWorkingSet
• abego_ : core::fragment::picking_old::vall::eval::ABEGOEval , protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData , protocols::forge::components::VarLengthBuild , protocols::frag_picker::frag_movers::FragSetFromH5Mover , protocols::jd2::parser::BluePrint
• ABEGOHashedFragmentStore_ : core::indexed_structure_store::ABEGOHashedFragmentStore , protocols::frag_picker::frag_movers::FragSetFromH5Mover , protocols::pose_length_moves::FixAllLoopsMover , protocols::pose_length_moves::NearNativeLoopCloser , protocols::pose_length_moves::PossibleLoop , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_moves::StructProfileMover
• abegoID : protocols::frag_picker::frag_movers::FragLocation
• abinitio_ : protocols::surface_docking::SurfaceDockingProtocol
• abinitio_mover_weight_ : protocols::topology_broker::TopologyClaimer
• abort_on_failed_loop_ : protocols::LoopRebuild
• abrelax_checkpoints_ : protocols::abinitio::AbrelaxApplication
• abs_deriv_dev : core::optimization::symmetry::MinDebug
• abs_deriv_dev_ : core::optimization::SimpleDerivCheckResult
• abs_stereochem_ : core::chemical::Atom
• absolute_ccd_tolerance_ : protocols::farna::movers::RNA_LoopCloser
• absX : protocols::pockets::CCluster::Cxyz
• absY : protocols::pockets::CCluster::Cxyz
• absZ : protocols::pockets::CCluster::Cxyz
• acc_ : protocols::md::MDBase
• acc_atm_ : core::scoring::hbonds::HBond
• acc_atm_is_backbone_ : core::scoring::hbonds::HBond
• acc_atm_is_protein_backbone_ : core::scoring::hbonds::HBond
• acc_chem_type2name_ : core::scoring::hbonds::HBondTypeManager
• acc_deriv : core::scoring::hbonds::HBondDerivs
• acc_dist_cutoff_ : protocols::features::WaterFeatures
• acc_occ_data_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• acc_res_ : core::scoring::hbonds::HBond
• acc_res_is_dna_ : core::scoring::hbonds::HBond
• acc_res_is_protein_ : core::scoring::hbonds::HBond
• acc_strength_lookup_ : core::scoring::hbonds::HBondDatabase
• acc_type_ : core::scoring::hbonds::HBEvalTuple
• accept : core::pack::annealer::RotSub
• accept_aborted_loops_ : protocols::loops::loop_mover::IndependentLoopMover
• accept_according_to_dunbrack_ : protocols::simple_moves::sidechain_moves::SidechainMover
• accept_blocks_missing_header_ : protocols::enzdes::AddOrRemoveMatchCsts
• accept_count : protocols::relax::SRelaxPose
• accept_counter_ : protocols::moves::TrialCounter , protocols::simple_moves::GenericMonteCarloMover
• accept_hists_ : protocols::backrub::BackrubSidechainMover
• accept_log_ : protocols::antibody::design::AntibodyDesignMover , protocols::carbohydrates::GlycanRelaxMover
• accept_rate_ : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• acceptance_history_ : protocols::jd2::archive::ArchiveBase
• ACCEPTANCE_REJECTION_HISTORY_LENGTH : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• ACCEPTED : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• accepted_ : protocols::moves::MoverStatistics
• accepted_history_head_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• accepted_rejected_substitution_history_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• acceptorList : protocols::sparta::PDB
• acceptors : protocols::sic_dock::EdgeStandScore
• acceptors_ : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• accepts_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• accepts_since_last_batch_ : protocols::jd2::archive::ArchiveBase
• access : core::scoring::sc::Atom
• accessible_dofs_ : core::environment::DofPassport
• accpt_pos_ : core::chemical::ResidueType
• accpt_pos_sc_ : core::chemical::ResidueType
• accum_ : core::scoring::packstat::Slice , core::scoring::packstat::trace
• accumulated_count_ : protocols::noesy_assign::PeakCalibrator
• accumulated_target_ : protocols::noesy_assign::PeakCalibrator
• accumulator_ : protocols::forge::remodel::RemodelMover
• accuracy_weight : core::scoring::rna::chemical_shift::ChemicalShiftData
• accuracy_weights_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• achiral_set_ : core::io::NomenclatureManager
• acid_base_ : protocols::simple_moves::IonizableResidue
• ACO_AOH_orb_Hpol_splines_ : core::scoring::orbitals::OrbitalsLookup
• actcoord_ : core::conformation::Residue
• actcoord_atoms_ : core::chemical::ResidueType
• actcoord_atoms_indices_ : core::chemical::ResidueType
• action_ : protocols::loophash::EXCN_DB_IO_Failed
• activated_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• active : protocols::relax::SRelaxPose
• active_ : protocols::optimize_weights::WeightRangeConstraint
• active_1benmeths_ : core::scoring::MinimizationNode
• active_1benmeths_ext_ : core::scoring::MinimizationNode
• active_1benmeths_std_ : core::scoring::MinimizationNode
• active_2b_score_types_ : core::scoring::EnergyGraph
• active_2benmeths_ : core::scoring::MinimizationEdge
• active_2benmeths_ext_ : core::scoring::MinimizationEdge
• active_2benmeths_std_ : core::scoring::MinimizationEdge
• active_angle_ : protocols::stepwise::sampler::MC_OneTorsion
• active_atom_tree_ : core::pack::scmin::ResidueAtomTreeCollection
• active_constraint_ : core::scoring::constraints::AmbiguousConstraint
• active_constraints_ : core::scoring::constraints::KofNConstraint , protocols::constraints_additional::AmbiguousMultiConstraint
• active_intrares2benmeths_ : core::scoring::MinimizationNode
• active_intrares2benmeths_ext_ : core::scoring::MinimizationNode
• active_intrares2benmeths_std_ : core::scoring::MinimizationNode
• active_peaks_ : protocols::noesy_assign::DistanceScoreMover
• active_pose_constraints_ : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• active_pucker_state_ : protocols::stepwise::sampler::rna::RNA_MC_Sugar
• active_residue_ : core::pack::scmin::ResidueAtomTreeCollection
• active_residue_atom_to_dofnode_index_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• active_residue_index_for_res_ : core::pack::scmin::SCMinMinimizerMap
• active_residues_ : core::pack::scmin::SCMinMinimizerMap
• active_restype_ : core::pack::scmin::ResidueAtomTreeCollection
• active_score_types_ : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• active_sequence_labels_ : protocols::topology_broker::FragmentClaimer
• active_site_grid_ : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::Matcher
• active_variables_ : protocols::optimize_weights::WrapperOptEMultifunc
• active_variables_this_dependent_dof_ : protocols::optimize_weights::WrapperOptEMultifunc
• activity : protocols::qsar::qsarOptData
• actual_cycles_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• actual_phosphate_move_list_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• actual_rep_cutoff_ : protocols::stepwise::screener::PartitionContactScreener
• adapt_graft_ : protocols::antibody::design::AntibodyDesignMover
• adaptation_period_ : protocols::simple_moves::GenericMonteCarloMover
• adaptive_ : protocols::simple_moves::GenericMonteCarloMover
• adaptive_movers_ : protocols::simple_moves::GenericMonteCarloMover
• add_base_pair_constraints_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• add_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::CyclizationMover
• add_cst_seed_ : protocols::seeded_abinitio::CAcstGenerator
• add_csts_to_pose_ : protocols::simple_moves::StructProfileMover
• add_delete_frequency_ : protocols::magnesium::MgMonteCarlo , protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• add_fuzzy_ : protocols::abinitio::HedgeArchive
• add_helix_capping_ : protocols::flxbb::LayerDesignOperation
• add_hetatm_ : protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• add_lead_zero_to_tag_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• add_ligand_to_pose_ : protocols::forge::constraints::InvrotTreeRCG
• add_log_to_pose_ : protocols::antibody::design::AntibodyDesignMover
• add_long_range_damping_ : core::scoring::etable::Etable
• add_membrane_mover_ : protocols::docking::membrane::MPDockingMover
• add_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• add_nbr_radius_ : protocols::ligand_docking::LigandArea
• add_non_init_chunks_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• add_observer_cache_segs_to_interface_ : protocols::enzdes::DetectProteinLigandInterface
• add_or_delete_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• add_original_ : core::optimization::GA_Minimizer
• add_peptide_plane_variants_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• add_probability_ : protocols::sewing::MonteCarloAssemblyMover
• add_proposal_density_factor_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• add_target_ : protocols::seeded_abinitio::SeedFoldTree
• add_target_to_pose_ : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• add_target_types_ : protocols::simple_moves::ModifyVariantTypeMover
• add_termini_ : protocols::cyclic_peptide::DeclareBond
• add_to_allowed_aas_ : protocols::toolbox::task_operations::ConservativeDesignOperation , protocols::toolbox::task_operations::MutationSetDesignOperation
• add_virt_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• add_virt_res_as_root_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• added_cutpoint_closed_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• additional_low_resolution_steps_ : protocols::docking::DockingProtocol
• additional_string_output_ : core::io::StructFileRep
• additional_task_operations_ : protocols::docking::DockTaskFactory
• addmem_ : protocols::membrane::MPQuickRelaxMover , protocols::relax::RangeRelaxMover
• address_ : protocols::canonical_sampling::mc_convergence_checks::PoolData
• addtime_ : protocols::simple_moves::DumpPdb
• adduct_name_ : core::chemical::Adduct
• adducts_ : core::pack::task::ResidueLevelTask_
• ADJ_Tab : protocols::sparta::Sparta::SpartaLib
• adjacent_bg_node_indices_ : core::pack::interaction_graph::FirstClassNode< V, E, G >
• adjacent_first_class_node_indices_ : core::pack::interaction_graph::BackgroundNode< V, E, G >
• adjacent_node_ : core::pack::interaction_graph::NodeBase
• adjacent_node_ind_ : core::pack::interaction_graph::NodeBase
• adjacent_nodes_ : core::pack::interaction_graph::BackgroundNode< V, E, G >
• adjbb_elec_scale_ : core::scoring::FACTSPotential
• adjbb_solv_scale_ : core::scoring::FACTSPotential
• adjbs_elec_scale_ : core::scoring::FACTSPotential
• adjbs_solv_scale_ : core::scoring::FACTSPotential
• adjFileName : protocols::sparta::Sparta::SpartaLib
• adp_strategy_ : core::scoring::cryst::PhenixInterface , protocols::cryst::FitBfactorsMover
• ads_sec_struct_ : protocols::surface_docking::FullatomRelaxMover
• affix_to_patch_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• affix_to_position_map_ : core::chemical::carbohydrates::CarbohydrateInfoManager
• after : protocols::denovo_design::task_operations::SurroundingSS
• after_minimization_reference_energies_ : protocols::optimize_weights::IterativeOptEDriver
• after_placement_filter_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• ag_ab_atomic_contacts_ : protocols::antibody::AntibodyFeatures
• aggregate_ : protocols::pack_daemon::MultistateFitnessFunction
• aggregate_function_ : protocols::multistate_design::MultiStateFitnessFunction
• ahd_cutoff_ : protocols::features::WaterFeatures
• AHdist_long_fade_lookup_ : core::scoring::hbonds::HBondDatabase
• AHdist_poly_lookup_ : core::scoring::hbonds::HBondDatabase
• AHdist_short_fade_lookup_ : core::scoring::hbonds::HBondDatabase
• Ai_ : core::scoring::FACTSResidueInfo
• aid : core::scoring::packstat::Sphere
• aigraph_ : core::io::pose_from_sfr::GeometricRenameIsomorphismCallback , core::io::pose_from_sfr::GeometricRenameVerticiesEquivalent
• Aindex_ : core::chemical::orbitals::AssignOrbitals
• akash_dyepos_ : protocols::anchored_design::AnchorMoversData
• algo_ : core::scoring::cryst::PhenixInterface , protocols::cryst::SetRefinementOptionsMover
• algorithm_ : protocols::loops::loop_mover::LoopCM , protocols::match::upstream::BuildSet
• algorithm_inputs_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• alias_ : core::chemical::AddAtomAlias
• aliases_ : protocols::denovo_design::components::StructureData
• align_ : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::protein_interface_design::movers::TopologyBrokerMover
• align_angle_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::topology::HelixPairing
• align_chunk_ : protocols::hybridization::ChunkTrialMover
• align_file_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• align_input_axes_to_symdof_axes_ : protocols::matdes::SymDofMover
• align_only_over_base_atoms_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• align_option_ : protocols::hybridization::ChunkTrialMover
• align_pose_ : protocols::stepwise::screener::AlignRMSD_Screener
• align_rmsd_screener_ : protocols::stepwise::screener::IntegrationTestBreaker
• align_set_ : protocols::comparative_modeling::AlignmentSet
• align_templates_to_pose_ : protocols::hybridization::CartesianHybridize
• align_to_native_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• align_to_pdbname_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• align_to_ss_only_ : protocols::hybridization::InsertChunkMover
• align_torsions_ : protocols::farna::fragments::FragmentLibrary
• align_trial_counter_ : protocols::hybridization::InsertChunkMover
• aligned_ : protocols::star::Extender
• alignment_ : protocols::comparative_modeling::ThreadingJob , protocols::simple_filters::RelativePoseFilter , protocols::star::Extender
• alignment_atom_id_map_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• alignment_file_ : protocols::toolbox::task_operations::AlignedThreadOperation
• alignment_res_string_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• alignments_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingJobInputter
• all_abego_ : protocols::frag_picker::quota::ABEGO_SS_Map , protocols::frag_picker::quota::ABEGO_SS_Pool
• all_ala_C : protocols::seeded_abinitio::GrowPeptides
• all_ala_N : protocols::seeded_abinitio::GrowPeptides
• all_atom_inds_ : protocols::match::output::SingleDownstreamResidueWriter
• all_atom_mode_ : protocols::ligand_docking::LigandArea
• all_atom_residue_depth_ : protocols::frag_picker::VallResidue
• all_bb_atoms_ : core::chemical::ResidueType
• all_bfactors_zero_ : protocols::match::BfactorMPM
• all_boltz_ : protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• all_build_points_ : protocols::match::Matcher
• all_bur_unsat_polars_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• all_cdr_loops : protocols::antibody_legacy::Antibody
• All_CSA_lines_ : core::scoring::ChemicalShiftAnisotropy
• All_DC_lines_ : core::scoring::DipolarCoupling
• all_dist_buf_ : protocols::noesy_assign::DistanceScoreMover
• all_dof_map_ : protocols::ub_e2c::ubi_e2c_modeler
• all_downstream_algorithms_ : protocols::match::Matcher
• all_downstream_builders_ : protocols::match::Matcher
• all_energies_ : protocols::toolbox::DecoySetEvaluation
• all_frames_ : protocols::topology_broker::DisulfJumpClaimer
• all_gap_ : protocols::toolbox::task_operations::CrystalContactsOperation
• all_Hbonds_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• all_hits_ : protocols::match::HitNeighborFinder
• all_inputs_ProQ2_ : core::scoring::methods::ProQ_Energy
• all_inputs_ProQM_ : core::scoring::methods::ProQ_Energy
• all_invrots_ : protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover
• all_jump_pairings_ : protocols::topology_broker::DisulfJumpClaimer
• all_lex_states : protocols::match::MatcherOutputStats
• all_loops_ : protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy
• all_loops_closed_ : protocols::loops::loop_mover::IndependentLoopMover
• all_lores_score_final_ : protocols::farna::RNA_FragmentMonteCarlo
• all_methods_ : core::scoring::ScoreFunction
• all_movable_ : protocols::seeded_abinitio::SegmentHybridizer
• all_mutants_ : protocols::pmut_scan::PointMutScanDriver
• all_nmer_pssms_ : core::scoring::methods::NMerPSSMEnergy
• all_nmer_svms_ : core::scoring::methods::NMerSVMEnergy
• all_pairings_ : protocols::jumping::DisulfPairingLibrary
• all_peptides_ : protocols::analysis::PeptideDeriverMarkdownStreamOutputter
• all_pose_to_output_pose_ID_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• all_pssm_data_ : protocols::optimize_weights::IterativeOptEDriver
• All_RDC_lines : core::scoring::ResidualDipolarCoupling_Rohl
• All_RDC_lines_ : core::scoring::ResidualDipolarCoupling
• all_rna_fragments_file_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::options::RNA_FragmentMonteCarloOptions
• all_rots_bb_ : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• all_sc_atoms_ : core::chemical::ResidueType
• all_seeds_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SwapSegment
• all_segments_ : protocols::sewing::Assembly
• all_ss_ : protocols::frag_picker::quota::ABEGO_SS_Map , protocols::frag_picker::quota::ABEGO_SS_Pool
• all_structs_ : protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper
• all_suites_ : core::pose::rna::RNA_SuiteName
• all_target_res_ : protocols::toolbox::match_enzdes_util::InvrotTarget
• all_unsat_polars_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• all_vs_bb_energies_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• all_vs_bb_energy_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• all_vs_bb_energy_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• all_water_weights_ : core::scoring::geometric_solvation::WaterWeightGridSet
• allcdr_map_ : protocols::antibody::CDRsMinPackMin
• allGroups_ : protocols::toolbox::task_operations::LinkResidues
• allocated_ : core::graph::NegSpaceElement< T >
• allow_all_aas_ : protocols::seeded_abinitio::SeedSetupMover , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• allow_anchor_repack_ : protocols::anchored_design::AnchorMoversData
• allow_base_pair_only_centroid_screen_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_base_pair_only_screen_ : protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker
• allow_bondangles_ : protocols::helical_bundle::parameters::BundleParameters
• allow_bondlengths_ : protocols::helical_bundle::parameters::BundleParameters
• allow_bulge_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• allow_bulge_at_chainbreak_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_chain_boundary_jump_partner_right_at_fixed_BP_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• allow_chi_copy_ : protocols::simple_moves::ReturnSidechainMover
• allow_chi_during_relax_ : protocols::forge::remodel::RemodelMover::instruction_flags
• allow_consecutive_bulges_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• allow_cyclic_ : protocols::denovo_design::connection::Connection
• allow_d_cys_ : protocols::denovo_design::DisulfidizeMover
• allow_delete_ : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• allow_design_ : protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• allow_design_around_ : protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::ThreadSequenceOperation
• allow_dihedrals_ : protocols::helical_bundle::parameters::BundleParameters
• allow_duplicates : protocols::environment::claims::ResidueElement
• allow_fixed_res_at_moving_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• allow_fragment_moves_in_bps_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• allow_insert_res_ : protocols::farna::setup::RNA_DeNovoParameters
• allow_internal_hinge_moves_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• allow_internal_local_moves_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• allow_l_cys_ : protocols::denovo_design::DisulfidizeMover
• allow_overlap_ : protocols::ligand_docking::CompoundTranslate
• allow_phosphate_virtualization_ : core::pack::task::rna::RNA_ResidueLevelTask
• allow_reading_cancelled_decoys_ : protocols::jd2::archive::Batch
• allow_rebuild_bulge_mode_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_repack_ : protocols::antibody::H3RefineCCD
• allow_repacking_ : protocols::toolbox::task_operations::SelectResiduesWithinChainOperation
• allow_scoring_ : core::scoring::MembraneTopology
• allow_split_off_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_submotif_split_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• allow_syn_pyrimidine_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• allow_tmh_scoring_ : core::scoring::MembraneTopology
• allow_variable_bond_geometry_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• allow_virtual_ : core::conformation::symmetry::SymmData
• allow_virtual_o2prime_hydrogens_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allow_virtual_side_chains_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• allowable_sequence_sep_ : core::scoring::methods::LinearChainbreakEnergy
• allowed_aas_ : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , protocols::simple_moves::DesignRepackMover
• allowed_aas_per_jump_ : protocols::protein_interface_design::movers::MapHotspot
• allowed_bulge_res_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• allowed_closure_attempts_ : protocols::forge::remodel::RemodelLoopMover
• allowed_deviation_ : protocols::simple_moves::StructProfileMover
• allowed_deviation_for_turn_type_id_ : protocols::features::strand_assembly::SandwichFeatures
• allowed_deviation_loops_ : protocols::simple_moves::StructProfileMover
• allowed_dof_helix_indices_ : protocols::helical_bundle::BundleGridSamplerHelper
• allowed_dof_jumps_ : core::conformation::symmetry::SymDof
• allowed_dof_types_ : protocols::helical_bundle::BundleGridSamplerHelper
• allowed_failure_before_extend_ : protocols::LoopRebuild
• allowed_failure_before_stop : protocols::LoopRebuild
• allowed_failure_before_stop_ : protocols::LoopRebuild
• allowed_positions_ : protocols::loops::loop_closure::kinematic_closure::KinematicWrapper
• allowed_res_types_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_res_types_pointers_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• allowed_residue_types_ : core::pack::task::ResidueLevelTask_
• allowed_separation_ : protocols::antibody::CloseOneCDRLoop , protocols::antibody_legacy::CloseOneMover
• allowed_seqpos_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• allowed_time_ : core::optimization::GA_Minimizer
• allowed_torsion_indices_ : protocols::helical_bundle::BackboneGridSamplerHelper
• allowed_types_ : protocols::dna::DnaInterfacePacker , protocols::motifs::BuildPosition
• allowSeqShiftMoves_ : protocols::rbsegment_relax::AutoRBMover
• AllowSlideJumpMap_ : protocols::simple_moves::symmetry::SymmetrySlider
• allowSSFragInserts_ : protocols::rbsegment_relax::AutoRBMover
• allprotein_tf_ : protocols::flexpep_docking::FlexPepDockingProtocol
• allRs_ : protocols::cryst::MakeLatticeMover
• allsc_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• allTs_ : protocols::cryst::MakeLatticeMover
• aln_ : protocols::comparative_modeling::Align_RotamerEvaluator , protocols::evaluation::AlignEvaluator , protocols::hybridization::HybridizeProtocol
• aln_files_ : protocols::protein_interface_design::filters::RmsdFilter
• alns : protocols::comparative_modeling::AlignmentCluster
• alns_ : protocols::jd2::InnerMultiThreadingJob
• alpha : core::optimization::lbfgs_iteration_data , core::scoring::fiber_diffraction::Hankel , protocols::protein_interface_design::Transformation , Transformation
• alpha_ : core::io::CrystInfo , core::scoring::CSA , core::scoring::FACTSRsdTypeInfo , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::dna::DNABase , protocols::rigid::WholeBodyRotationMover , protocols::simple_moves::UniformRotationMover , protocols::stepwise::sampler::rigid_body::EulerAngles
• alpha_atom_names_ : core::scoring::dna::DNATorsionPotential
• alpha_beta_pattern_ : protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::ncbb::SecStructMinimizeMultiFunc
• alpha_components_ : core::scoring::dna::DNATorsionPotential
• alpha_fade_ : core::scoring::rna::RNA_TorsionPotential
• alpha_potential_ : core::scoring::rna::RNA_TorsionPotential
• alphabet_ : core::sequence::ChemicalShiftSequence , core::sequence::SequenceProfile
• alphamax : core::pose::rna::RNA_SuiteName
• alphamin : core::pose::rna::RNA_SuiteName
• alphas_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• already_prepped_for_simA_ : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• already_virtualized_res_list_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• alt : core::scoring::sc::_PROBE
• alt_bg_bg_exhpobeolap_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• alt_codes_ : core::io::NomenclatureManager
• alt_dots_cache_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• alt_e_up_to_date_ : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_energy_ : protocols::flexpack::interaction_graph::FlexbbEdge
• alt_rot_inds_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alt_rots_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alt_sc_centroid_ : core::pack::interaction_graph::SimpleNode
• alt_sc_radius_ : core::pack::interaction_graph::SimpleNode
• alt_state_atom_atom_overlaps_ : core::pack::interaction_graph::HPatchEdge< V, E, G >
• alt_state_being_considered_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• alt_state_dots_matches_current_state_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_energy_ : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• alt_state_exolap_hphobes_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G >
• alt_state_exp_hphobes_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_inv_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_rotamer_dots_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G >
• alt_state_sparse_mat_info_ : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode
• alt_state_total_hASA_ : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• alternate_one_body_energy_ : core::pack::interaction_graph::SimpleNode
• alternate_pose_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alternate_pose_energy_ : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• alternate_residue_ : core::pack::interaction_graph::SimpleNode
• alternate_state_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_info_ : protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_is_being_considered_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_one_body_energy_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_total_energy_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• alternate_state_two_body_energies_ : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode
• altitude_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• altitude_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• altitude_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern
• altLoc : core::io::AtomInformation , core::pose::PDBInfo::AtomRecord
• always_use_dssp_ : core::select::residue_selector::SecondaryStructureSelector
• am_ : core::fragment::picking_old::vall::eval::ABEGOEval
• amb_hnq_ : protocols::relax::AtomCoordinateCstMover
• aminoAcidList : protocols::forge::remodel::LineObject
• amplitude : core::chemical::rna::GaussianParameter
• amplitude_ : protocols::dna::DNABase
• aN : protocols::sparta::Sparta::SpartaLib
• ana_deriv_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• analytic_etable_evaluation : core::init::pre_talaris_2013_behavior_settings , core::scoring::etable::EtableOptions
• analytic_parameters_ : core::scoring::etable::Etable
• aname1_ : protocols::enzdes::DiffAtomSasaFilter
• aname2_ : protocols::enzdes::DiffAtomSasaFilter
• anb : core::scoring::packstat::CavityBall
• ancestor_name_ : core::chemical::ChangeAncestory
• anchor_ : core::scoring::func::MixtureFunc , protocols::anchored_design::AnchorMoversData
• anchor_at_res1_ : protocols::membrane::MembranePositionFromTopologyMover
• anchor_atom_dest_ : protocols::comparative_modeling::StealLigandMover
• anchor_atom_id_ : protocols::seeded_abinitio::CoordinateCst
• anchor_atom_name_ : core::pack::rotamer_set::WaterAnchorInfo
• anchor_atom_source_ : protocols::comparative_modeling::StealLigandMover
• anchor_chain_ : protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer
• anchor_id_ : protocols::viewer::ConformationViewer
• anchor_insert_only_ : protocols::hybridization::InsertChunkMover
• anchor_loop_index_ : protocols::anchored_design::AnchorMoversData
• anchor_noise_constraints_mode_ : protocols::anchored_design::AnchorMoversData
• anchor_offset_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::multistate_design::PartitionAggregateFunction< T > , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• anchor_positions_ : protocols::hybridization::HybridizeFoldtreeDynamic
• anchor_res_ : protocols::protein_interface_design::movers::SetAtomTree , protocols::seeded_abinitio::CoordinateCst
• anchor_reses_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• anchor_residue_ : core::conformation::symmetry::SymmData , core::pack::rotamer_set::WaterAnchorInfo , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::MetalloClaimer
• anchor_residues_ : protocols::hybridization::AllResiduesChanged
• anchor_resnum_ : protocols::protein_interface_design::movers::TaskAwareCsts
• anchor_rsd_ : protocols::membrane::AddMembraneMover
• anchor_specified_ : protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree
• anchor_sugar_modeling_ : protocols::stepwise::screener::AnchorSugarScreener
• anchor_sugar_solution_number_ : protocols::stepwise::screener::AnchorSugarScreener
• anchor_via_constraints_ : protocols::anchored_design::AnchorMoversData
• anchored_graft_mover_ : protocols::antibody::AntibodyCDRGrafter , protocols::antibody::design::AntibodyDesignMover
• anchorfile_ : protocols::anchored_design::Anchor
• anchors_ : protocols::protein_interface_design::filters::BoltzmannFilter , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree
• ang123_ : protocols::toolbox::match_enzdes_util::LigandConformer
• ang_cst_ : core::scoring::constraints::BackboneStubConstraint
• ang_D1D2D3_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_U1D2_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• ang_U1D2_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• ang_U2D1_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• ang_U2D1_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• angle : core::scoring::packstat::trace , protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral , protocols::ligand_docking::Transform_info , protocols::make_rot_lib::CentroidRotNum
• angle_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData , protocols::matdes::GetRBDOFValues , protocols::membrane::FlipMover , protocols::membrane::TiltMover , protocols::rigid::RollMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::sidechain_moves::SetChiMover
• angle_atom_ : core::chemical::AddConnect , core::scoring::methods::GoapRsdType
• angle_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• angle_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• angle_cutoff_ : protocols::features::ModelFeatures
• ANGLE_CUTOFF_HIGH : core::scoring::methods::LK_SigmoidalFunc
• ANGLE_CUTOFF_LOW : core::scoring::methods::LK_SigmoidalFunc
• ANGLE_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• angle_deltas_ : protocols::matdes::SymDofMover
• angle_disp_ : protocols::backrub::BackrubSegment
• angle_exponent_ : core::select::util::SelectResiduesByLayer
• angle_magnitude_ : protocols::rigid::RigidBodyDeterministicSpinMover
• angle_max_ : protocols::membrane::MPQuickRelaxMover , protocols::relax::RangeRelaxMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::bb_sampler::SmallBBSampler , protocols::stepwise::sampler::MC_OneTorsion , protocols::surface_docking::FullatomRelaxMover
• angle_min_ : protocols::stepwise::sampler::MC_OneTorsion
• angle_params_ : core::scoring::methods::ResidueCartBondedParameters
• angle_resl_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• angle_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• angle_sd1_ : core::scoring::rna::RNA_SugarCloseEnergy
• angle_sd2_ : core::scoring::rna::RNA_SugarCloseEnergy
• angle_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
• angle_shift_factor_ : core::select::util::SelectResiduesByLayer
• angle_sigma2_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• angle_steps_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• angle_table_ : core::scoring::methods::GoapEnergy
• angle_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• angle_tolerance_ : protocols::fldsgn::SheetConstraintGenerator
• angle_wt_ : protocols::simple_filters::SymmetricMotifFilter
• angle_wts_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• angleA_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• angleB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• anglelist : protocols::cartesian::MolecularDynamics
• angles : core::scoring::carbohydrates::CHIDihedralSamplingData , protocols::loophash::BBData
• angles_ : core::fragment::BBTorsionAndAnglesSRFD , core::scoring::sasa::LeGrandSasa , protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler , protocols::pockets::PocketConstraint
• angles_range_max_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• angles_range_min_ : protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler
• angsplines_ : core::scoring::CenRotEnvPairPotential
• angstroms : protocols::ligand_docking::Translate_info
• angstroms_ : protocols::ligand_docking::TetherLigand
• angth : protocols::kinmatch::KRSQuery
• animate_ : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• aniso_ : protocols::electron_density::VoxelSpacingRefinementMover
• ann : protocols::environment::EnvClaimBroker::BrokerResult
• ann_ : protocols::environment::EnvClaimBroker , protocols::environment::Environment
• ANN_CS_OUTPUT_FULL : protocols::sparta::Sparta::SpartaLib
• ANN_IN_MTX : protocols::sparta::ANN , protocols::sparta::Sparta::SpartaLib
• ANN_IN_MTX_LEVEL1 : protocols::sparta::ANN
• ANN_IN_MTX_LEVEL2 : protocols::sparta::ANN
• ANN_OUT_MTX_LEVEL1 : protocols::sparta::ANN
• ANN_OUT_MTX_LEVEL2 : protocols::sparta::ANN
• annotated_sequence_ : protocols::topology_broker::claims::SequenceClaim
• annotated_sequence_used_for_atom_id_maps_ : protocols::stepwise::modeler::align::StepWisePoseAligner
• annotations_ : core::io::rna::RDAT , protocols::environment::ProtectedConformation
• anomer_ : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_ : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_index_ : core::chemical::carbohydrates::CarbohydrateInfo
• anomeric_carbon_name_ : core::chemical::carbohydrates::CarbohydrateInfo
• ANTI : core::scoring::dssp::Pairing
• anti_ : protocols::abinitio::AlternativePairings
• antibody_build_ : protocols::antibody_legacy::CDRH3Modeler
• antibody_in_ : protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler
• antibody_info_ : protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol
• antibody_refine_ : protocols::antibody_legacy::CDRH3Modeler
• antibody_region_to_enum_ : protocols::antibody::AntibodyEnumManager
• antibody_region_to_string_ : protocols::antibody::AntibodyEnumManager
• antigen_chains_ : protocols::antibody::constraints::ParatopeSiteConstraintMover
• antipar : core::scoring::dssp::StrandPairing
• antiparallel_weight_ : core::scoring::SecondaryStructureWeights
• any_intrares_energies_ : core::scoring::ScoreFunction
• AObondedatoms_ : core::chemical::orbitals::AssignOrbitals
• AOD_orb_orb_splines_ : core::scoring::orbitals::OrbitalsLookup
• AOdist_ : core::chemical::orbitals::AssignOrbitals
• AOH_Haro_scOrbH_splines_ : core::scoring::orbitals::OrbitalsLookup
• AOH_Hpol_bbOrbH_splines_ : core::scoring::orbitals::OrbitalsLookup
• AOH_Hpol_scOrbH_splines_ : core::scoring::orbitals::OrbitalsLookup
• AOhybridization_ : core::chemical::orbitals::AssignOrbitals
• APBS_CONFIG_EXT : core::scoring::PoissonBoltzmannPotential , protocols::pb_potential::SetupPoissonBoltzmannPotential
• APBS_DX_EXT : core::scoring::PoissonBoltzmannPotential , protocols::pb_potential::SetupPoissonBoltzmannPotential
• apbs_path_ : core::scoring::PoissonBoltzmannPotential
• APBS_PQR_EXT : core::scoring::PoissonBoltzmannPotential , protocols::pb_potential::SetupPoissonBoltzmannPotential
• apfc_list_ : core::scoring::custom_pair_distance::RespairInteractions
• apol_calcenergy : core::scoring::APBSConfig::I_PARAM
• apol_calcforce : core::scoring::APBSConfig::I_PARAM
• apolar_ : core::pack::task::operation::ResidueTypeFilter
• append_ : protocols::simple_moves::LoadPDBMover
• append_n_residues_ : protocols::ncbb::oop::OopCreatorMover
• applied_fullatom_pert_ : protocols::ub_e2c::ubi_e2c_modeler
• apply_ambiguous_constraints_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• apply_centroid_mode_ : protocols::antibody_legacy::CDRH3Modeler
• apply_default_commands_to_inserts_ : core::pack::task::operation::ReadResfileAndObeyLengthEvents
• apply_fullatom_mode_ : protocols::antibody_legacy::CDRH3Modeler
• apply_large_frags_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• apply_probability_ : protocols::rosetta_scripts::ParsedProtocol
• apply_residue_alternative_sampler_ : protocols::stepwise::screener::SampleApplier
• apply_self_energies_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• apply_to_centroid_ : protocols::abinitio::ResolutionSwitcher
• apply_vdw_cut_ : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• apply_virtual_res_variant_at_dinucleotide_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• approved_ : protocols::topology_broker::claims::DofClaim
• approximate_vdw_radii_ : core::scoring::AtomVDW
• arc_ : protocols::jd2::archive::SortPredicate
• archive_rank_ : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor
• archived_starting_task_ : protocols::forge::remodel::RemodelDesignMover
• arcs_ : core::scoring::packstat::trace
• area : core::scoring::packstat::CavityBall , core::scoring::packstat::LR_AtomData , core::scoring::packstat::LR_MP_AtomData , core::scoring::sc::_DOT , core::scoring::sc::_RESULTS
• area_cav_ball_required_exposed : core::scoring::packstat::SasaOptions
• arg_sweep_cutoff_ : protocols::enzdes::DetectProteinLigandInterface
• arg_sweep_interface_ : protocols::enzdes::DetectProteinLigandInterface
• argc_ : protocols::rpc::BasicCmdLineInit
• argstring_ : core::pack::task::TARGET
• argv_ : protocols::rpc::BasicCmdLineInit
• aro_specified_ : core::pack::task::EX
• aroC_scale_factor_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• aroma_ : core::chemical::Bond
• aromatic_ : core::pack::task::operation::ResidueTypeFilter
• aromatic_dG_fraction : protocols::analysis::InterfaceData
• aromatic_dSASA_fraction : protocols::analysis::InterfaceData
• aromatic_motifs_ : protocols::motifs::MotifDnaPacker
• aromatic_nres : protocols::analysis::InterfaceData
• around_shell_ : protocols::simple_filters::EnergyPerResidueFilter
• array : core::scoring::APBSConfig::I_PARAM , core::scoring::APBSConfig::R_PARAM
• array_ : core::graph::Array0< T > , core::graph::ArrayPoolElement< T > , core::graph::NegSpaceElement< T > , core::scoring::EnergyEdge , core::scoring::packstat::Array2D
• array_blocks_ : core::graph::ArrayPool< T >
• array_size_ : core::graph::ArrayPool< T >
• asked_for_feedback_ : protocols::mpi_refinement::MPI_Refine_Master
• assembly_scorefxn_ : protocols::sewing::AssemblyMover
• assert_jump_point_in_fixed_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• assign_new_cluster_tag : protocols::toolbox::ClusterOptions
• assign_state_to_all_nodes_immediately_ : core::pack::annealer::RotamerAssigningAnnealer
• assigned_num_ : protocols::loophash::LoopHashLibrary
• assigned_string_ : protocols::loophash::LoopHashLibrary
• assignment_ : protocols::noesy_assign::EXCN_AssignmentNotFound
• assignments_ : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::CrossPeak::Spin , protocols::noesy_assign::CrossPeakList
• assume_atom_ids_invariant_ : protocols::stepwise::modeler::align::StepWiseClusterer
• assume_non_stem_is_loop : protocols::farna::setup::RNA_DeNovoPoseSetup
• astype1_ : protocols::simple_filters::AtomicDistanceFilter
• astype2_ : protocols::simple_filters::AtomicDistanceFilter
• asymm_only_ : protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities
• asymmetric_res_ : protocols::topology_broker::SymmetryClaimer
• asymmetric_unit_ : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• at1_type_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• at2_type_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• at3_type_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• at_inds_ : protocols::match::downstream::AtomGeometrySecMatchRPE
• atcs_for_residues_ : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• atm1_ : protocols::simple_filters::AngleToVector
• atm2_ : protocols::simple_filters::AngleToVector
• atm_ : core::chemical::ResetBondLength
• atm_coords_ : core::io::silent::BinarySilentStruct
• atmid_ : core::scoring::methods::GoapRsdType
• atmname_using_ : core::scoring::methods::GoapRsdType
• atms : core::scoring::elec::ElecGroup
• atms_ : protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint
• atom : core::scoring::packstat::Circle
• ATOM : core::scoring::packstat::SimplePDB_Atom
• atom : core::scoring::sc::_ATOM_RADIUS , core::scoring::sc::_DOT , core::scoring::sc::Atom
• atom1 : core::id::BondID , core::id::NamedStubID , core::id::StubID , protocols::denovo_design::components::BondInfo , protocols::environment::claims::JumpElement
• atom1_ : core::chemical::AddBond , core::chemical::AddBondType , core::chemical::AddChi , core::chemical::ChangeBondType , core::chemical::RedefineChi , core::chemical::sdf::MolFileIOBond , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::lkball::WaterBuilder , core::scoring::RDC , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::simple_moves::TorsionDOFMover , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::topology_broker::claims::JumpClaim
• atom2 : core::id::BondID , core::id::NamedStubID , core::id::StubID , protocols::denovo_design::components::BondInfo , protocols::environment::claims::JumpElement
• atom2_ : core::chemical::AddBond , core::chemical::AddBondType , core::chemical::AddChi , core::chemical::ChangeBondType , core::chemical::RedefineChi , core::chemical::sdf::MolFileIOBond , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::lkball::WaterBuilder , core::scoring::RDC , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::simple_moves::TorsionDOFMover , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::topology_broker::claims::JumpClaim
• atom2csa_map_ : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• atom2dc_map_ : core::scoring::methods::DipolarCouplingEnergy
• atom2rdc_map_ : core::scoring::methods::ResidualDipolarCouplingEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• atom3 : core::id::NamedStubID , core::id::StubID
• atom3_ : core::chemical::AddChi , core::chemical::RedefineChi , core::scoring::constraints::AngleConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::CSA , core::scoring::lkball::WaterBuilder , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::simple_moves::TorsionDOFMover , protocols::toolbox::match_enzdes_util::EnzCstTemplateRes , protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms
• atom4_ : core::chemical::AddChi , core::chemical::RedefineChi , core::scoring::constraints::DihedralConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::simple_moves::TorsionDOFMover
• atom_ : core::chemical::AddConnectAndTrackingVirt , core::chemical::AddConnectDeleteChildProton , core::chemical::ChangeAncestory , core::chemical::DeleteChildProton , core::chemical::ReplaceProtonWithBromine , core::chemical::ReplaceProtonWithChlorine , core::chemical::ReplaceProtonWithEthyl , core::chemical::ReplaceProtonWithFluorine , core::chemical::ReplaceProtonWithHydroxyl , core::chemical::ReplaceProtonWithIodine , core::chemical::ReplaceProtonWithMethoxy , core::chemical::ReplaceProtonWithMethyl , core::chemical::ReplaceProtonWithTrifluoromethyl , core::chemical::SetICoor , core::id::NamedAtomID , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::trie::RotamerDescriptorAtom< AT, CPDAT > , core::scoring::trie::TrieNode< AT, CPDATA > , protocols::noesy_assign::EXCN_UnknownResonance , protocols::noesy_assign::Resonance
• atom_2_residue_connection_map_ : core::chemical::ResidueType
• atom_aliases_ : core::chemical::ResidueType
• atom_atom_distance : protocols::ligand_docking::rdf::AtomPairData
• atom_atom_overlap_dist_cutoff_ : protocols::stepwise::screener::ResidueContactScreener
• atom_base_ : core::chemical::ResidueType
• atom_base_indices_ : core::chemical::ResidueType
• atom_bin_size_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• atom_bur_unsat_ : protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator
• atom_center_ : protocols::cyclic_peptide::CreateAngleConstraint
• atom_charge_ : core::chemical::Adduct
• atom_counts_ : core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache
• atom_delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• atom_dependent_calibration_ : protocols::noesy_assign::PeakAssignmentParameters
• atom_derivatives_ : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• atom_equiv_ : protocols::comparative_modeling::ThreadingMover
• atom_f1_f2s_ : core::scoring::methods::LK_hack
• atom_ff_types_ : core::scoring::saxs::SAXSEnergy
• atom_flags_ : protocols::frag_picker::scores::AtomBasedConstraintsScore
• atom_gaussian_value : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• atom_geom_rpes_ : protocols::match::downstream::GeometrySecMatchRPE
• atom_has_orbitals_ : core::chemical::AtomType
• atom_Hbonds_ : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• atom_hydrophobic_ : protocols::fldsgn::MyAtom
• atom_id : protocols::cartesian::CartesianAtom
• atom_id_ : core::id::DOF_ID , core::kinematics::tree::Atom_ , protocols::seeded_abinitio::CoordinateCst
• atom_id_1 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• atom_id_2 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_Bond , protocols::cartesian::MD_HarmonicDihedral
• atom_id_3 : protocols::cartesian::MD_Angle , protocols::cartesian::MD_HarmonicDihedral
• atom_id_4 : protocols::cartesian::MD_HarmonicDihedral
• atom_id_domain_map_ : core::pose::copydofs::CopyDofs
• atom_id_map_ : core::pose::copydofs::CopyDofs
• atom_id_mapper_ : protocols::toolbox::AtomLevelDomainMap
• atom_id_mapper_to_vanilla_chunk_pose_ : protocols::farna::libraries::ChunkSet
• atom_id_mask_ : protocols::farna::libraries::ChunkSet
• atom_ids_ : core::conformation::UltraLightResidue , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::pockets::PocketConstraint , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• atom_ids_for_coordinates_ : protocols::match::downstream::TargetRotamerCoords
• atom_ids_in_res_ : protocols::toolbox::AtomID_Mapper
• atom_index_ : core::scoring::custom_pair_distance::resatom_and_func_struct
• atom_index_to_relevant_atom_index_ : protocols::features::AtomAtomPairFeatures
• atom_indices_ : core::optimization::CartesianMinimizerMap , protocols::electron_density::BfactorMultifunc
• atom_inds_for_restype_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• atom_is_repulsive_ : core::chemical::AtomType
• atom_is_virtual_ : core::chemical::AtomType
• atom_it_ : protocols::sewing::ModelConstIterator< T > , protocols::sewing::ModelIterator< T >
• atom_level_domain_map_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::farna::libraries::RNA_ChunkLibrary , protocols::farna::movers::RNA_FragmentMover , protocols::farna::movers::RNA_JumpMover , protocols::farna::movers::RNA_LoopCloser , protocols::farna::movers::RNA_Minimizer , protocols::farna::RNA_FragmentMonteCarlo , protocols::simple_moves::ConstrainToIdealMover , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::modeler::StepWiseMinimizer
• atom_level_domain_map_input_ : protocols::farna::movers::RNA_Minimizer
• atom_limit_ : protocols::ligand_docking::AtomCountFilter
• atom_map_ : core::scoring::hbonds::HBondSet , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::PerSphereAccumulator , protocols::hybridization::InsertChunkMover , protocols::qsar::qsarMap
• atom_map_init_ : core::scoring::hbonds::HBondSet
• ATOM_MASK : core::scoring::electron_density::ElectronDensity
• ATOM_MASK_PADDING : core::scoring::electron_density::ElectronDensity
• atom_name : core::scoring::rna::chemical_shift::ChemicalShiftData
• atom_name1_ : protocols::farna::libraries::RNA_PairingTemplate
• atom_name2_ : protocols::farna::libraries::RNA_PairingTemplate
• atom_name_ : core::chemical::AddAtom , core::chemical::Adduct , core::chemical::AppendMainchainAtom , core::chemical::DeleteActCoordAtom , core::chemical::DeleteAtom , core::chemical::DeleteMetalbindingAtom , core::chemical::PrependMainchainAtom , core::chemical::SetAtomicCharge , core::chemical::SetAtomType , core::chemical::SetBackboneHeavyatom , core::chemical::SetFormalCharge , core::chemical::SetMMAtomType , core::chemical::SetNbrAtom , core::chemical::SetPolymerConnectAtom , core::conformation::AtomGraphVertexData , core::pose::UnrecognizedAtomRecord , core::scoring::packing::PoseBalls , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::qsar::qsarPoint , protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• atom_name_id_cache_ : core::chemical::ResidueDatabaseIO
• atom_name_to_vd_ : core::chemical::ResidueType
• atom_names_list_ : core::pose::MiniPose
• atom_names_soft_ : core::chemical::ResidueTypeFinder
• atom_needs_update_from_wide_ : core::scoring::NeighborList
• atom_neighbors_ : core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList
• atom_num_ : core::scoring::packing::PoseBalls , core::scoring::packing::PoseBallsLite
• atom_numbers_for_backbone_score_calculations_ : core::scoring::rna::RNA_LowResolutionPotential
• atom_numbers_for_mg_calculation_ : core::scoring::rna::RNA_ScoringInfo
• atom_numbers_for_vdw_calculation_ : core::scoring::rna::RNA_ScoringInfo
• atom_numbers_sugar_ : core::scoring::rna::data::RNA_DataBackboneEnergy
• atom_numbers_sugar_coarse_ : core::scoring::rna::data::RNA_DataBackboneEnergy
• atom_pair_constraint_contact_map_ : protocols::frag_picker::FragmentPicker
• atom_pair_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• atom_pair_constraint_weight_ : protocols::idealize::IdealizeMover
• atom_pair_weight_ : protocols::antibody::design::GeneralAntibodyModeler
• atom_parent_ : core::scoring::packing::PoseBalls
• atom_pointer_ : core::kinematics::AtomTree
• atom_positions_ : core::pack::rotamers::SingleLigandRotamerLibrary
• atom_property_status_ : core::chemical::AtomProperties
• atom_radii_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::upstream::BuildSet
• atom_radius_squared_ : core::conformation::AtomGraphVertexData
• atom_required_in_active_site_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• atom_res_idx_ : core::scoring::methods::dfire::DFIRE_Potential
• atom_sasa_ : core::pack::interaction_graph::RotamerDots , core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::scoring::sasa::SasaCalc
• atom_scores : core::scoring::packing::HolesResult
• atom_semiexpl_score_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• atom_set_ : core::scoring::etable::Etable
• atom_shadowed_ : core::chemical::ResidueType
• atom_shadowed_indices_ : core::chemical::ResidueType
• atom_subset_ : core::scoring::sasa::SasaCalc
• atom_tree_ : core::conformation::Conformation
• atom_tree_collection_ : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• atom_tree_diff_ : protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::AtomTreeDiffJobOutputter
• atom_tree_minimizer_ : protocols::stepwise::modeler::StepWiseMinimizer
• atom_tree_representatives_ : core::pack::scmin::ResidueAtomTreeCollection
• atom_tree_uptodate_ : core::pack::scmin::ResidueAtomTreeCollection
• atom_two_body_energies_ : core::scoring::SplitUnfoldedTwoBodyPotential
• atom_type : protocols::pockets::CCluster::Cxyz
• atom_type_ : core::scoring::MultipoleParameter , core::scoring::packing::PoseBalls , core::scoring::vdwaals::VDWAtom
• atom_type_dbio_ : protocols::features::AtomTypesFeatures
• atom_type_index_ : core::chemical::Atom , core::chemical::AtomTypeSet , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MMAtomTypeSet
• atom_type_is_charged_ : core::scoring::lkball::LK_BallEnergy
• atom_type_label_set_used_ : core::scoring::SplitUnfoldedTwoBodyPotential
• atom_type_name_ : core::chemical::AddAtom , core::chemical::Adduct , core::chemical::orbitals::OrbitalType , core::chemical::SetAtomType
• atom_type_set_name_ : core::scoring::AtomVDW , core::scoring::vdwaals::VDW_Energy
• atom_type_set_ptr_ : core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy
• atom_type_set_tag_ : core::chemical::ResidueLoaderOptions
• atom_type_sets_ : core::chemical::ChemicalManager
• atom_types_ : core::chemical::AcceptorAtomFilter , core::chemical::APolarHydrogenFilter , core::chemical::AromaticAtomFilter , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::HeavyAtomFilter , core::chemical::HeavyAtomWithHydrogensFilter , core::chemical::HeavyAtomWithPolarHydrogensFilter , core::chemical::HydrogenAtomFilter , core::chemical::PolarHydrogenFilter , core::chemical::ResidueType , core::chemical::ResidueTypeSet
• atom_unsat_ : protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator
• atom_vdw_ : core::scoring::AtomVDW , core::scoring::methods::HybridVDW_Energy , core::scoring::ScoringManager , core::scoring::vdwaals::VDW_Energy , protocols::scoring::InterchainPotential
• atom_vdw_atom_type_set_name_ : core::scoring::methods::EnergyMethodOptions
• atom_weight_stored : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• atom_weights_ : core::scoring::lkball::LKB_ResidueInfo , core::scoring::lkball::lkbtrie::LKBAtom
• atom_weights_map_ : core::scoring::lkball::LKB_ResidueInfo
• atomA1_ : core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint
• atomA2_ : core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint
• atomA3_ : core::scoring::constraints::DihedralPairConstraint
• atomA4_ : core::scoring::constraints::DihedralPairConstraint
• atomB1_ : core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint
• atomB2_ : core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint
• atomB3_ : core::scoring::constraints::DihedralPairConstraint
• atomB4_ : core::scoring::constraints::DihedralPairConstraint
• atomdesg1_ : protocols::simple_filters::AtomicDistanceFilter
• atomdesg2_ : protocols::simple_filters::AtomicDistanceFilter
• atomdesg_ : protocols::protein_interface_design::filters::HbondsToAtomFilter
• atomic_interaction_cutoff_ : core::scoring::geometric_solvation::DatabaseOccSolEne , core::scoring::vdwaals::VDWTrieEvaluator
• atomic_number_ : core::chemical::Element
• atomic_orbitals_nonbinding_ : core::chemical::gasteiger::GasteigerAtomTypeData
• atomic_radius_ : core::scoring::GenBornResidueInfo
• atomid_ : core::kinematics::AtomWithDOFChange
• atomID_ : protocols::normalmode::NormalMode
• AtomID_to_atomnbr_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• atomid_to_csts_ : core::scoring::constraints::MultiConstraint
• atomlist_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• atomName : protocols::sparta::CORdata
• atomname_ : protocols::contact_map::ContactPartner
• atomnames_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• atomno : protocols::sewing::HashValue
• atomNo : protocols::sparta::RingData
• atomno1_ : core::scoring::SmallAtNb
• atomno2_ : core::scoring::SmallAtNb
• atomno_ : core::chemical::ICoorAtomID , core::chemical::ResidueConnection , core::id::AtomID , core::scoring::AtomNeighbor , protocols::scoring::ImplicitFastClashCheck , protocols::sewing::SewAtom
• atomNum : protocols::sparta::CORdata
• atomRec : core::pose::PDBInfo::ResidueRecord
• atoms : core::scoring::sc::MolecularSurfaceCalculator , protocols::environment::EnvClaimBroker::BrokeredJumpData
• ATOMS : protocols::sparta::PDB
• atoms : protocols::sparta::RingData
• atoms1_ : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• atoms2_ : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• atoms_ : core::chemical::AtomTypeSet , core::chemical::MMAtomTypeSet , core::conformation::Residue , core::io::ResidueInformation , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , core::scoring::packstat::SimplePDB , core::scoring::trie::RotamerDescriptor< AT, CPDAT > , protocols::environment::claims::JumpClaim , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• atoms_123_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::toolbox::match_enzdes_util::LigandConformer
• atoms_downstream_ : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• atoms_in_patches_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator
• atoms_last_controlled_by_chi_ : core::chemical::ResidueType
• atoms_per_residue_ : protocols::helical_bundle::parameters::BundleParameters
• atoms_representing_chis_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• atoms_representing_ds_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• atoms_representing_thetas_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• atoms_to_atoms_ : protocols::toolbox::task_operations::CrystalContactsOperation
• atoms_to_compare_ : protocols::match::output::DownstreamRMSEvaluator
• atoms_to_dofid_ : core::pack::scmin::CartSCMinMinimizerMap
• atoms_to_superimpose_on_ : protocols::enzdes::EnzdesBaseProtocol
• atoms_to_update_ : core::scoring::NeighborList
• atoms_upstream_ : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate
• atoms_with_orb_index_ : core::chemical::ResidueType
• atoms_within_one_bond_of_a_residue_connection_ : core::chemical::ResidueType
• atoms_within_two_bonds_of_a_residue_connection_ : core::chemical::ResidueType
• AtomSurfaceFullList : protocols::sparta::PDB
• AtomSurfacePartList : protocols::sparta::PDB
• atr : protocols::ligand_docking::Ligand_info
• atr_cutoff_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::screener::PartitionContactScreener
• atr_radius_ : protocols::qsar::scoring_grid::ClassicGrid
• atr_rep_checker_ : protocols::stepwise::legacy::screener::ProteinAtrRepScreener , protocols::stepwise::legacy::screener::RNA_AtrRepScreener , protocols::stepwise::screener::BulgeApplier
• atr_rep_checker_with_instantiated_sugar_ : protocols::stepwise::screener::AnchorSugarScreener
• atr_rep_checkers_for_anchor_sugar_models_ : protocols::stepwise::screener::AnchorSugarScreener
• atr_rep_screen_ : protocols::stepwise::options::StepWiseBasicOptions
• atr_rep_screen_for_docking_ : protocols::stepwise::options::StepWiseBasicOptions
• atr_rep_screening_scorefxn_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• atr_weight_ : core::scoring::etable::EtableEvaluator
• ats123_reqd_in_active_site_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• attach_boinc_ghost_observer_ : protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber
• attached_ : core::pose::datacache::ObserverCache
• attached_H_begin_ : core::chemical::ResidueType
• attached_H_end_ : core::chemical::ResidueType
• attached_res_ : protocols::stepwise::monte_carlo::mover::Attachment
• attachment_type_ : protocols::stepwise::monte_carlo::mover::Attachment
• attachments_ : protocols::stepwise::monte_carlo::mover::StepWiseMove
• attempt_closure_cutoff_ : protocols::farna::movers::RNA_LoopCloser
• atten : core::scoring::sc::Atom
• attractive : core::scoring::etable::AtomPairEnergy
• atype2holes_ : core::scoring::packing::HolesParams
• auction_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• auction_results_ : protocols::protein_interface_design::movers::PlacementAuctionMover
• auto_adjust_factorA_ : protocols::simple_moves::BBGaussianMover
• auto_clash_ : core::scoring::motif::ResPairMotifQuery
• auto_cuts : protocols::environment::EnvClaimBroker::BrokerResult
• auto_cuts_ : protocols::environment::AutoCutData
• auto_design : protocols::forge::remodel::RemodelData
• auto_frag_insertion_weight_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• auto_loops_ : protocols::protein_interface_design::movers::LoopRemodel
• auto_mm_ : protocols::seeded_abinitio::SegmentHybridizer
• auto_range_ : protocols::matdes::SymDofMover
• auto_tune_ : protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• auto_update_ : core::scoring::NeighborList
• autofilter_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• autofilter_score_quantile_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• autofoldtree_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::symmetric_docking::SymDockProtocol
• autoinitialize_ : protocols::anchored_design::AnchoredDesignMover
• automatic_ : protocols::forge::remodel::RemodelMover::instruction_flags
• automatic_connection_ : protocols::protein_interface_design::movers::TryRotamers
• automatic_distance_cutoff_ : protocols::protein_interface_design::movers::AddChainBreak
• automatic_repacking_definition_ : protocols::simple_moves::DesignRepackMover
• automode_scorecut_ : protocols::hybridization::CartesianSampler
• autoset_wt_ : protocols::cryst::SetCrystWeightMover
• autotemp_ : protocols::moves::MonteCarlo
• available_moves_ : protocols::simple_moves::oop::OopRandomPuckMover
• available_nodes_ : protocols::sewing::Assembly
• available_seg_list_ : protocols::simple_moves::BBGaussianMover
• average_change_in_rama_score_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• average_change_in_torsion_angle_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• avg : protocols::make_rot_lib::running_average_pair
• avg_rho_obs : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• avoid_building_any_rotamers_dueto_native_ : protocols::match::upstream::ProteinUpstreamBuilder
• avoid_sc_hbonds_ : core::scoring::hbonds::hbtrie::HBCPData
• ax_ : 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
• ax_init_ : core::optimization::MinimizerOptions
• axis_ : protocols::matdes::GetRBDOFValues , protocols::membrane::FlipMover , protocols::rigid::RollMover , protocols::rigid::WholeBodyRotationMover , protocols::simple_moves::UniformRotationMover
• axis_bin_width_ : core::scoring::rna::RNA_LowResolutionPotential
• axis_num_bins_ : core::scoring::rna::RNA_LowResolutionPotential
• axis_origin_ : core::conformation::symmetry::VirtualCoordinate
• axis_x_ : core::conformation::symmetry::VirtualCoordinate
• axis_y_ : core::conformation::symmetry::VirtualCoordinate
• axs : protocols::kinmatch::KRSQuery
• azmiuth_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• azmiuth_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• azmiuth_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern