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• AA : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamer_set::WaterAnchorInfo , core::pack::task::PackerTask , core::scoring::OmegaTether , core::scoring::Rama2BOffset , core::scoring::Ramachandran2B , core::scoring::Ramachandran
• AAsIter : core::chemical::ResidueTypeSet
• ABEGOManager : core::fragment::picking_old::vall::eval::ABEGOEval
• ABEGOManagerOP : core::fragment::picking_old::vall::eval::ABEGOEval
• AllMethods : core::scoring::ScoreFunction
• AllMethodsIterator : core::scoring::ScoreFunction
• angle_parameter : core::scoring::methods::ResidueCartBondedParameters
• AngleInfo : core::fragment::BBTorsionAndAnglesSRFD
• Atom : core::kinematics::AtomTree
• AtomCOP : core::kinematics::AtomTree
• AtomID : 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::Energies , core::scoring::func::FourPointsFunc , core::scoring::func::XYZ_Func , core::scoring::hbonds::HBondSet
• 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
• AtomIndices : core::conformation::Residue
• AtomList : core::coarse::Translator , core::fragment::DownJumpSRFD , core::id::NamedStubID , core::scoring::rna::RNA_AtomVDW
• AtomMap : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T >
• AtomOP : core::kinematics::AtomTree
• AtomPairConstraintOP : core::scoring::constraints::Obsolet_NamedAtomPairConstraint
• AtomRecords : core::pose::PDBInfo
• Atoms : core::kinematics::tree::Atom , core::scoring::constraints::AmbiguousNMRDistanceConstraint
• 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
• AtomWeightsMap : core::scoring::methods::LKB_ResidueInfo