- a -

• a : core::scoring::packstat::PointPair
• a0_ : core::scoring::FACTSRsdTypeInfo
• a1_ : core::scoring::FACTSRsdTypeInfo
• a2_ : core::scoring::FACTSRsdTypeInfo
• a3_ : core::scoring::FACTSRsdTypeInfo
• A_ : core::pose::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_bins : core::scoring::dna::DirectReadoutPotential
• a_ids_ : core::scoring::saxs::SAXSEnergy
• a_kappa : core::scoring::disulfides::FullatomDisulfideParams13
• a_logA : core::scoring::disulfides::FullatomDisulfideParams13
• a_mu : core::scoring::disulfides::FullatomDisulfideParams13
• aa1_ : core::scoring::motif::ResPairMotif
• AA1name : core::scoring::constraints::ResidueTypeLinkingConstraint
• aa2_ : core::scoring::motif::ResPairMotif
• AA2name : core::scoring::constraints::ResidueTypeLinkingConstraint
• aa_ : core::chemical::ResidueType , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::VallResidue , core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary , core::pack::rotamer_set::WaterAnchorInfo , core::scoring::motif::Xfres
• aa_block_for_baserotamer_ : core::pack::rotamer_set::ContinuousRotamerSet
• aa_block_for_samplingrotamer_ : core::pack::rotamer_set::ContinuousRotamerSet
• aa_encoder_ : core::scoring::methods::NMerSVMEnergy
• aa_for_rotblock_ : core::pack::rotamer_set::ContinuousRotamerSet
• aa_libraries_ : core::pack::dunbrack::RotamerLibrary
• aa_map_ : core::chemical::ResidueTypeSet
• aa_neighbors_for_edges_ : core::pack::interaction_graph::LinearMemNode
• 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_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_submatrix_history_list_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• 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
• AAname : core::scoring::constraints::NonResidueTypeConstraint , core::scoring::constraints::ResidueTypeConstraint
• aas_ : core::chemical::Selector_AA
• aas_at_grid : core::scoring::dna::DirectReadoutPotential
• aas_defined_ : core::chemical::ResidueTypeSet
• abase2_ : core::chemical::ResidueType
• abase2_deriv : core::scoring::hbonds::HBondDerivs
• abase2_indices_ : core::chemical::ResidueType
• abase_deriv : core::scoring::hbonds::HBondDerivs
• abego_ : core::fragment::picking_old::vall::eval::ABEGOEval
• abegoHashedFragmentStore_ : core::scoring::methods::VallLookbackPotential
• abs_deriv_dev : core::optimization::symmetry::MinDebug
• abs_deriv_dev_ : core::optimization::SimpleDerivCheckResult
• 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_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
• 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_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
• 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
• accuracy_weight : core::scoring::rna::chemical_shift::ChemicalShiftData
• accuracy_weights_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• ACO_AOH_orb_Hpol_splines_ : core::scoring::orbitals::OrbitalsLookup
• actcoord_ : core::conformation::Residue
• actcoord_atoms_ : core::chemical::ResidueType
• actcoord_atoms_indices_ : core::chemical::ResidueType
• 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_atom_tree_ : core::pack::scmin::ResidueAtomTreeCollection
• active_constraint_ : core::scoring::constraints::AmbiguousConstraint
• active_constraints_ : core::scoring::constraints::KofNConstraint
• active_intrares2benmeths_ : core::scoring::MinimizationNode
• active_intrares2benmeths_ext_ : core::scoring::MinimizationNode
• active_intrares2benmeths_std_ : core::scoring::MinimizationNode
• 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
• add_long_range_damping : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• add_original_ : core::optimization::GA_Minimizer
• adduct_name_ : core::chemical::Adduct
• adducts_ : core::pack::task::ResidueLevelTask_
• 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
• adp_strategy_ : core::scoring::cryst::PhenixInterface
• 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::pdb::GeometricRenameIsomorphismCallback , core::io::pdb::GeometricRenameVerticiesEquivalent
• Aindex_ : core::chemical::orbitals::AssignOrbitals
• algo_ : core::scoring::cryst::PhenixInterface
• alias_ : core::chemical::AddAtomAlias
• all_bb_atoms_ : core::chemical::ResidueType
• All_CSA_lines_ : core::scoring::ChemicalShiftAnisotropy
• All_DC_lines_ : core::scoring::DipolarCoupling
• all_inputs_ProQ2_ : core::scoring::methods::ProQ_Energy
• all_inputs_ProQM_ : core::scoring::methods::ProQ_Energy
• all_methods_ : core::scoring::ScoreFunction
• all_nmer_pssms_ : core::scoring::methods::NMerPSSMEnergy
• all_nmer_svms_ : core::scoring::methods::NMerSVMEnergy
• All_RDC_lines : core::scoring::ResidualDipolarCoupling_Rohl
• All_RDC_lines_ : core::scoring::ResidualDipolarCoupling
• all_rots_bb_ : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• all_sc_atoms_ : core::chemical::ResidueType
• all_suites_ : core::pose::rna::RNA_SuiteName
• all_water_weights_ : core::scoring::geometric_solvation::WaterWeightGridSet
• allocated_ : core::graph::NegSpaceElement< T >
• allow_phosphate_virtualization_ : core::pack::task::rna::RNA_ResidueLevelTask
• allow_scoring_ : core::scoring::MembraneTopology
• allow_tmh_scoring_ : core::scoring::MembraneTopology
• allow_virtual_ : core::conformation::symmetry::SymmData
• allowable_sequence_sep_ : core::scoring::methods::LinearChainbreakEnergy
• allowed_aas_ : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT
• allowed_dof_jumps_ : core::conformation::symmetry::SymDof
• allowed_residue_types_ : core::pack::task::ResidueLevelTask_
• allowed_time_ : core::optimization::GA_Minimizer
• alpha : core::optimization::lbfgs_iteration_data , core::scoring::fiber_diffraction::Hankel
• alpha_ : core::pose::CrystInfo , core::scoring::CSA , core::scoring::FACTSRsdTypeInfo
• alpha_atom_names_ : core::scoring::dna::DNATorsionPotential
• 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
• alt : core::scoring::sc::_PROBE
• alt_bg_bg_exhpobeolap_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• alt_dots_cache_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• 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_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
• 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
• 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
• 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
• 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
• altLoc : core::io::pdb::AtomInformation , core::pose::PDBInfo::AtomRecord
• am_ : core::fragment::picking_old::vall::eval::ABEGOEval
• amplitude : core::chemical::rna::GaussianParameter
• 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
• anb : core::scoring::packstat::CavityBall
• anchor_ : core::scoring::func::MixtureFunc
• anchor_atom_name_ : core::pack::rotamer_set::WaterAnchorInfo
• anchor_residue_ : core::conformation::symmetry::SymmData , core::pack::rotamer_set::WaterAnchorInfo
• ang_cst_ : core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint
• angle : core::scoring::packstat::trace
• angle_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• angle_atom_ : core::chemical::AddConnect , core::scoring::methods::GoapRsdType
• angle_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• ANGLE_CUTOFF_HIGH : core::scoring::methods::LK_SigmoidalFunc
• ANGLE_CUTOFF_LOW : core::scoring::methods::LK_SigmoidalFunc
• ANGLE_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• angle_params_ : core::scoring::methods::ResidueCartBondedParameters
• angle_resl_ : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• angle_sd1_ : core::scoring::rna::RNA_SugarCloseEnergy
• angle_sd2_ : core::scoring::rna::RNA_SugarCloseEnergy
• angle_sd_ : core::scoring::rna::RNA_SugarCloseEnergy
• angle_table_ : core::scoring::methods::GoapEnergy
• angles_ : core::fragment::BBTorsionAndAnglesSRFD , core::scoring::sasa::LeGrandSasa
• angsplines_ : core::scoring::CenRotEnvPairPotential
• animate_ : core::conformation::ResidueKinWriter
• annotations_ : core::io::rna::RDAT
• 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
• 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
• APBS_DX_EXT : core::scoring::PoissonBoltzmannPotential
• apbs_path_ : core::scoring::PoissonBoltzmannPotential
• APBS_PQR_EXT : core::scoring::PoissonBoltzmannPotential
• 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
• apply_default_commands_to_inserts_ : core::pack::task::operation::ReadResfileAndObeyLengthEvents
• approximate_vdw_radii_ : core::scoring::AtomVDW
• 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
• argstring_ : core::pack::task::TARGET
• aro_specified_ : core::pack::task::EX
• aroC_scale_factor_ : core::scoring::carbon_hbonds::CarbonHBondPotential
• aroma_ : core::chemical::Bond
• aromatic_ : core::pack::task::operation::ResidueTypeFilter
• 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 >
• assign_state_to_all_nodes_immediately_ : core::pack::annealer::RotamerAssigningAnnealer
• atcs_for_residues_ : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• atm_coords_ : core::io::silent::BinarySilentStruct
• atmid_ : core::scoring::methods::GoapRsdType
• atmname_using_ : core::scoring::methods::GoapRsdType
• atms : core::scoring::elec::ElecGroup
• 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
• atom1_ : core::chemical::AddBond , core::chemical::AddBondType , core::chemical::AddChi , 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::methods::WaterBuilder , core::scoring::RDC
• atom2 : core::id::BondID , core::id::NamedStubID , core::id::StubID
• atom2_ : core::chemical::AddBond , core::chemical::AddBondType , core::chemical::AddChi , 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::methods::WaterBuilder , core::scoring::RDC
• atom2csa_map_ : core::scoring::methods::ChemicalShiftAnisotropyEnergy
• atom2dc_map_ : core::scoring::methods::DipolarCouplingEnergy
• atom2rdc_map_ : core::scoring::methods::ResidualDipolarCouplingEnergy
• 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::methods::WaterBuilder
• atom4_ : core::chemical::AddChi , core::chemical::RedefineChi , core::scoring::constraints::DihedralConstraint
• atom_ : 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 >
• atom_2_residue_connection_map_ : core::chemical::ResidueType
• atom_aliases_ : core::chemical::ResidueType
• atom_base_ : core::chemical::ResidueType
• atom_base_indices_ : core::chemical::ResidueType
• 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_derivatives_ : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• atom_f1_f2s_ : core::scoring::methods::LK_hack
• atom_ff_types_ : core::scoring::saxs::SAXSEnergy
• atom_gaussian_value : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• atom_has_orbitals_ : core::chemical::AtomType
• atom_id_ : core::id::DOF_ID , core::kinematics::tree::Atom_
• atom_id_domain_map_ : core::pose::copydofs::CopyDofs
• atom_id_map_ : core::pose::copydofs::CopyDofs
• atom_ids_ : core::conformation::UltraLightResidue , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint
• atom_index_ : core::scoring::custom_pair_distance::resatom_and_func_struct
• atom_indices_ : core::optimization::CartesianMinimizerMap
• atom_is_virtual_ : core::chemical::AtomType
• atom_map_ : core::scoring::hbonds::HBondSet , core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator , core::scoring::packstat::PerSphereAccumulator
• 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_name_ : core::chemical::AddAtom , core::chemical::Adduct , core::chemical::AppendMainchainAtom , 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
• atom_name_id_cache_ : core::chemical::ResidueDatabaseIO
• atom_name_to_vd_ : core::chemical::ResidueType
• atom_names_list_ : core::pose::MiniPose
• 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_energy_ : core::scoring::constraints::ConstraintEdge
• atom_parent_ : core::scoring::packing::PoseBalls
• atom_pointer_ : core::kinematics::AtomTree
• atom_radius_squared_ : core::conformation::AtomGraphVertexData
• 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_set_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• 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_representatives_ : core::pack::scmin::ResidueAtomTreeCollection
• atom_tree_uptodate_ : core::pack::scmin::ResidueAtomTreeCollection
• atom_type_ : core::scoring::packing::PoseBalls , core::scoring::vdwaals::VDWAtom
• atom_type_index_ : core::chemical::Atom , core::chemical::AtomTypeSet , core::chemical::gasteiger::GasteigerAtomTypeSet , core::chemical::MMAtomTypeSet
• atom_type_is_charged_ : core::scoring::methods::LK_BallEnergy
• 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_vdw_ : core::scoring::AtomVDW , core::scoring::methods::HybridVDW_Energy , core::scoring::ScoringManager , core::scoring::vdwaals::VDW_Energy
• atom_vdw_atom_type_set_name_ : core::scoring::methods::EnergyMethodOptions
• atom_weight_stored : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• atom_weights_ : core::scoring::methods::LKB_ResidueInfo
• atom_weights_map_ : core::scoring::methods::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
• 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_to_atomnbr_ : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• AtomID_to_Csts_ : core::scoring::constraints::MultiConstraint
• atomnames_ : core::scoring::rna::chemical_shift::RNA_CS_residue_parameters
• atomno1_ : core::scoring::SmallAtNb
• atomno2_ : core::scoring::SmallAtNb
• atomno_ : core::chemical::ICoorAtomID , core::chemical::ResidueConnection , core::id::AtomID , core::scoring::AtomNeighbor
• atomRec : core::pose::PDBInfo::ResidueRecord
• atoms : core::io::pdb::ResidueInformation , core::scoring::sc::MolecularSurfaceCalculator
• atoms1_ : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• atoms2_ : core::scoring::constraints::AmbiguousNMRDistanceConstraint
• atoms_ : core::chemical::AtomTypeSet , core::chemical::MMAtomTypeSet , core::conformation::Residue , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , core::scoring::packstat::SimplePDB , core::scoring::trie::RotamerDescriptor< AT, CPDAT >
• atoms_last_controlled_by_chi_ : core::chemical::ResidueType
• atoms_representing_chis_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• atoms_representing_ds_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• atoms_representing_thetas_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• atoms_to_dofid_ : core::pack::scmin::CartSCMinMinimizerMap
• atoms_to_update_ : core::scoring::NeighborList
• 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
• atr_weight_ : core::scoring::etable::EtableEvaluator
• attached_H_begin_ : core::chemical::ResidueType
• attached_H_end_ : core::chemical::ResidueType
• atten : core::scoring::sc::Atom
• attractive : core::scoring::etable::AtomPairEnergy
• atype2holes_ : core::scoring::packing::HolesParams
• auto_clash_ : core::scoring::motif::ResPairMotifQuery
• auto_update_ : core::scoring::NeighborList
• avg_rho_obs : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• avoid_sc_hbonds_ : core::scoring::hbonds::hbtrie::HBCPData
• ax_init_ : core::optimization::MinimizerOptions
• 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