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• AA : core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::task::PackerTask , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::simple_moves::MinimalRotamer , protocols::toolbox::SelectResiduesByLayer , protocols::fldsgn::potentials::AACompositionEnergy , core::scoring::OmegaTether , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::flxbb::DesignTask , core::pack::rotamer_set::WaterAnchorInfo , core::scoring::Ramachandran , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::PNatAAOptERotamerData , core::scoring::Ramachandran2B , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::DDGMutationOptEData
• AAsIter : core::chemical::ResidueTypeSet
• ABEGOManager : core::fragment::picking_old::vall::eval::ABEGOEval
• ABEGOManagerOP : core::fragment::picking_old::vall::eval::ABEGOEval
• AcceptHistoryQueue : protocols::jd2::archive::ArchiveBase
• ActiveVoxelSet : protocols::match::OccupiedSpaceHash
• Address : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• 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
• AllStructureDistanceBoundVector : protocols::noesy_assign::DistanceScoreMover
• angle_parameter : core::scoring::methods::ResidueCartBondedParameters
• AngleInfo : core::fragment::BBTorsionAndAnglesSRFD
• ArgIndices : protocols::pack_daemon::VectorFunction , protocols::pack_daemon::VectorFunction2
• ArithmeticASTExpression : protocols::pack_daemon::IterativeVectorExpression
• ArithmeticASTExpressionOP : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• Atom : core::kinematics::AtomTree , protocols::fldsgn::NcontactsCalculator
• AtomByResList : protocols::noesy_assign::PeakAssignmentResidueMap
• AtomCOP : core::kinematics::AtomTree
• AtomID : core::scoring::constraints::FourPointsFunc , protocols::match::downstream::DownstreamBuilder , core::conformation::Conformation , core::conformation::symmetry::SymmetryInfo , core::kinematics::AtomTree , core::kinematics::MinimizerMapBase , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::optimization::AtomNode , core::optimization::DOF_Node , core::optimization::MinimizerMap , core::pose::Pose , core::scoring::constraints::Constraint , core::scoring::constraints::Constraints , core::scoring::constraints::ConstraintSet , core::scoring::constraints::XYZ_Func , core::scoring::Energies , core::scoring::hbonds::HBondSet , protocols::match::output::DownstreamRMSEvaluator
• AtomID_Mask : core::kinematics::MoveMap , core::kinematics::tree::Atom , core::scoring::Energies , core::conformation::Conformation , core::kinematics::AtomTree
• AtomIDs : core::conformation::symmetry::SymmetryInfo , core::optimization::DOF_Node , core::kinematics::AtomTree
• AtomIndices : core::conformation::Residue
• AtomIndsForRestypeMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• AtomList : core::fragment::DownJumpSRFD , protocols::jumping::PairingTemplate , protocols::noesy_assign::PeakAssignmentResidueMap , core::coarse::Translator , protocols::noesy_assign::MethylNames , protocols::jumping::DisulfTemplate , core::id::NamedStubID , core::scoring::rna::RNA_AtomVDW
• AtomMap : core::id::DOF_ID_Map< T > , core::id::AtomID_Map< T >
• AtomNameList : protocols::forge::build::ConnectRight
• AtomOP : core::kinematics::AtomTree
• AtomPairConstraintList : protocols::abinitio::Template
• AtomPairConstraintOP : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• AtomRecords : core::pose::PDBInfo
• Atoms : core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::kinematics::tree::Atom
• Atoms_ConstIterator : core::kinematics::tree::Atom
• Atoms_Iterator : core::kinematics::tree::Atom
• AtomToken : core::coarse::Rule
• AtomTree : core::conformation::Conformation
• AtomTreeOP : core::conformation::Conformation
• AtomType : core::conformation::Residue
• AtomTypeSets : core::chemical::ChemicalManager