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• AA : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::flxbb::DesignTask , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData , protocols::simple_moves::MinimalRotamer , protocols::toolbox::SelectResiduesByLayer
• AAProbabilities : protocols::antibody::design::ResidueProbDesignOperation
• 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
• AllStructureDistanceBoundVector : protocols::noesy_assign::DistanceScoreMover
• AngleMap : protocols::sparta::Sparta::SpartaLib
• ANN_Matrix : protocols::sparta::ANN
• ANN_Vector : protocols::sparta::ANN
• AnnotatingSelectors : protocols::environment::claims::EnvClaim
• ArgIndices : protocols::pack_daemon::VectorFunction2 , protocols::pack_daemon::VectorFunction
• ArithmeticASTExpression : protocols::pack_daemon::IterativeVectorExpression
• ArithmeticASTExpressionOP : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• Atom : protocols::fldsgn::NcontactsCalculator
• Atom2ANN_MatrixMap : protocols::sparta::Sparta::SpartaLib
• AtomByResList : protocols::noesy_assign::PeakAssignmentResidueMap
• AtomEntries : protocols::sparta::PDB
• AtomID : protocols::match::downstream::DownstreamBuilder , protocols::match::output::DownstreamRMSEvaluator
• AtomIndsForRestypeMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• AtomList : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::noesy_assign::MethylNames , protocols::noesy_assign::PeakAssignmentResidueMap
• AtomNameList : protocols::forge::build::ConnectRight , protocols::sparta::Sparta::SpartaLib
• AtomPairConstraintList : protocols::abinitio::Template
• AtomsMap : protocols::sparta::PDB