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• AA : core::pack::dunbrack::cenrot::CenrotLibrary , core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamer_set::WaterAnchorInfo , core::pack::task::PackerTask , core::scoring::dna::DNA_EnvPairPotential , core::scoring::OmegaTether , core::scoring::PointWaterPotential , core::scoring::Ramachandran2B , core::scoring::Ramachandran , core::scoring::RamaPrePro , core::select::util::SelectResiduesByLayer , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::flxbb::DesignTask , protocols::minimization_packing::MinimalRotamer , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData
• AACompositionEnergySetup : core::energy_methods::AACompositionEnergy
• AACompositionEnergySetupCOP : core::energy_methods::AACompositionEnergy
• AACompositionEnergySetupOP : core::energy_methods::AACompositionEnergy
• AAFrequencyMap : protocols::denovo_design::task_operations::AAFrequencies
• AAProbabilities : protocols::task_operations::ResidueProbDesignOperation
• AAs : protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• Abego : protocols::denovo_design::components::IdealAbegoGenerator , protocols::denovo_design::task_operations::ConsensusLoopDatabase
• ABEGOManager : core::fragment::picking_old::vall::eval::ABEGOEval
• ABEGOManagerOP : core::fragment::picking_old::vall::eval::ABEGOEval
• Abegos : protocols::denovo_design::components::IdealAbegoGenerator
• AbegoToLoopAAsMap : protocols::denovo_design::task_operations::ConsensusLoopDatabase
• AcceptHistoryQueue : protocols::jd2::archive::ArchiveBase
• action_pair : core::pack::task::operation::DesignRestrictions
• ActiveVoxelSet : protocols::match::OccupiedSpaceHash
• AID : protocols::sic_dock::Rose
• Alignment : protocols::comparative_modeling::MultiThreadingMover
• Alignments : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingJobInputter
• AllMethods : core::scoring::ScoreFunction
• AllMethodsIterator : core::scoring::ScoreFunction
• Allocator : protocols::mean_field::jagged_array< T, A >
• allocator_type : protocols::mean_field::jagged_array< T, A >
• AllStructureDistanceBoundVector : protocols::noesy_assign::DistanceScoreMover
• angle_parameter : core::energy_methods::ResidueCartBondedParameters
• AngleInfo : core::fragment::BBTorsionAndAnglesSRFD
• AngleMap : protocols::sparta::Sparta::SpartaLib
• ANN_Matrix : protocols::sparta::ANN
• ANN_Vector : protocols::sparta::ANN
• AnnealableGraphBaseCOP : protocols::minimization_packing::PackRotamersMover
• AnnealableGraphBaseOP : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer , core::pack::annealer::FixbbPwatSimAnnealer , core::pack::annealer::FixbbSimAnnealer , core::pack::annealer::SequenceSymmetricAnnealer , core::pack::annealer::SmartFixbbSimAnnealer , protocols::minimization_packing::PackRotamersMover
• AnnotatingSelectors : protocols::environment::claims::EnvClaim
• ArchitectCreatorMap : protocols::denovo_design::architects::DeNovoArchitectFactory
• ArgIndices : protocols::pack_daemon::VectorFunction2 , protocols::pack_daemon::VectorFunction
• ArithmeticASTExpression : protocols::pack_daemon::IterativeVectorExpression
• ArithmeticASTExpressionOP : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• Array1aa : protocols::indexed_structure_store::SegmentSequenceProfileResult
• ArrayXaa : protocols::indexed_structure_store::SegmentSequenceProfileResult
• AssemblyRequirementCreatorMap : protocols::sewing::requirements::AssemblyRequirementFactory
• AssemblyScorerCreatorMap : protocols::sewing::scoring::AssemblyScorerFactory
• Atom : core::kinematics::AtomTree , protocols::fldsgn::NcontactsCalculator
• Atom2ANN_MatrixMap : protocols::sparta::Sparta::SpartaLib
• atom_sasa_score_map : core::pack::guidance_scoreterms::sap::SapConstraintHelper
• atom_sasa_score_value : core::pack::guidance_scoreterms::sap::SapConstraintHelper
• atom_within_5_value : core::pack::guidance_scoreterms::sap::SapConstraintHelper
• AtomByResList : protocols::noesy_assign::PeakAssignmentResidueMap
• AtomCOP : core::kinematics::AtomTree
• AtomEntries : protocols::sparta::PDB
• AtomID : core::conformation::Conformation , core::conformation::symmetry::SymmetryInfo , core::kinematics::AtomTree , core::kinematics::MinimizerMapBase , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::optimization::DOF_Node , core::optimization::MinimizerMap , core::pose::Pose , core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::Energies , core::scoring::func::FourPointsFunc , core::scoring::func::XYZ_Func , core::scoring::hbonds::HBondSet , core::scoring::hbonds::NPDHBondSet , protocols::match::downstream::DownstreamBuilder , protocols::match::output::DownstreamRMSEvaluator , protocols::rna::movers::ErraserMinimizerMover
• AtomID_Mask : core::conformation::Conformation , core::kinematics::AtomTree , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::scoring::Energies
• AtomIDs : core::conformation::symmetry::SymmetryInfo , core::kinematics::AtomTree , core::optimization::DOF_Node , protocols::denovo_design::movers::RotateSegmentMover
• AtomIndices : core::conformation::Residue
• AtomIndsForRestypeMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• AtomList : core::fragment::DownJumpSRFD , core::id::NamedStubID , core::scoring::rna::RNA_AtomVDW , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::noesy_assign::MethylNames , protocols::noesy_assign::PeakAssignmentResidueMap
• AtomMap : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• AtomNameList : protocols::forge::build::ConnectRight , protocols::sparta::Sparta::SpartaLib
• AtomNameMap : protocols::constraint_generator::HydrogenBondInfo
• AtomNameSet : protocols::constraint_generator::HydrogenBondConstraintGenerator
• AtomOP : core::kinematics::AtomTree
• AtomPairConstraintList : protocols::abinitio::Template
• AtomPairConstraintOP : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• AtomRecords : core::pose::PDBInfo
• AtomRenamingMap : core::chemical::MergeBehaviorManager
• Atoms : core::kinematics::tree::Atom , core::scoring::constraints::AmbiguousNMRDistanceConstraint , protocols::denovo_design::movers::RotateSegmentMover
• Atoms_ConstIterator : core::kinematics::tree::Atom
• Atoms_Iterator : core::kinematics::tree::Atom
• AtomsMap : protocols::sparta::PDB
• AtomTree : core::conformation::Conformation
• AtomTreeOP : core::conformation::Conformation
• AtomType : core::conformation::Residue
• AtomTypeSets : core::chemical::ChemicalManager
• Authors : core::io::HeaderInformation