- a -

• access_ptr : protocols::jd2::utility::pointer::access_ptr< T >

- c -

• CClusterSet : protocols::pockets::CCluster
• ClosureProblem : protocols::kinematic_closure::ClosureSolution
• ClosureSolution : protocols::kinematic_closure::ClosureProblem
• ComparisonGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid

- d -

• DarcParticleSwarmMinimizer : protocols::pockets::FingerprintBase , protocols::pockets::PlaidFingerprint
• DofUnlock : protocols::environment::ProtectedConformation

- e -

• EggshellGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• EnvClaimBroker : protocols::environment::ClaimingMover , protocols::environment::ProtectedConformation
• Environment : protocols::environment::ClaimingMover , protocols::environment::ProtectedConformation
• EnzConstraintParameters : protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• EnzCstTemplateRes : protocols::toolbox::match_enzdes_util::EnzCstTemplateResAtoms , protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache

- f -

• FingerprintMultifunc : protocols::pockets::DarcElectrostaticsBase , protocols::pockets::DelphiElectrostatics , protocols::pockets::FingerprintBase , protocols::pockets::PlaidFingerprint
• FragmentLookupFilterCreator : protocols::indexed_structure_store::filters::FragmentLookupFilter
• FragmentScoreManager : protocols::frag_picker::scores::FragmentScoreMap

- g -

• GunnCostTest : protocols::simple_moves::GunnCost

- h -

• HotspotStub : protocols::hotspot_hashing::HotspotStubSet
• HotspotStubSet : protocols::hotspot_hashing::HotspotStub

- j -

• JD2ResourceManagerCreator : protocols::jd2::JD2ResourceManager
• JobDistributorFactory : protocols::jd2::archive::ArchiveManager , protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MPIWorkPartitionJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::ShuffleFileSystemJobDistributor

- m -

• Memento : protocols::kinematic_closure::ClosureProblem
• MPI_WorkUnitManager : protocols::wum::WorkUnitBase
• MPI_WorkUnitManager_Slave : protocols::wum::WorkUnitBase
• Mutant : protocols::pmut_scan::MutationData

- n -

• NonPlaidFingerprint : protocols::pockets::EggshellGrid

- o -

• operator!= : protocols::id::AlignmentID , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::sic_dock::Rose
• operator* : protocols::sic_dock::Rose
• operator< : protocols::branch_angle::BranchParam1 , protocols::branch_angle::BranchParam2 , protocols::farna::BasePairStepSequence , protocols::farna::BasePairType , protocols::id::AlignmentID
• operator<< : protocols::abinitio::PairingStatistics , protocols::antibody::Ab_TemplateInfo , protocols::antibody::AntibodyInfo , protocols::antibody::AntibodyModelerProtocol , protocols::antibody::CDRsMinPackMin , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::SnugDock , protocols::antibody::SnugDockProtocol , protocols::canonical_sampling::AsyncMPITemperingBase , protocols::docking::DockingLowRes , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::farna::BasePairStep , protocols::farna::BasePairStepSequence , protocols::features::helixAssembly::HelicalFragment , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::Helix , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::Loop , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::Strand , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::id::AlignmentID , protocols::jd2::archive::Batch , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::jumping::JumpSample , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycleContainer , protocols::loops::loop_mover::refine::RepackTrial , protocols::loops::loop_mover::refine::ShearMinCCDTrial , protocols::loops::loop_mover::refine::SmallMinCCDTrial , protocols::loops::Loops , protocols::loops::LoopsFileIO , protocols::match::output::MatchScoreWriter , protocols::motif_hash::MotifHash , protocols::motif_hash::ResPairMotif , protocols::motif_hash::XformScore , protocols::motif_hash::Xfres , protocols::motifs::Motif , protocols::motifs::MotifLibrary , protocols::motifs::SingleMotif , protocols::moves::MoverContainer , protocols::moves::TrialMover , protocols::pmut_scan::Mutant , protocols::pmut_scan::MutationData , protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs2::PcsEnergyParameterManager , protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::scoring::methods::pcs2::PcsInputCenter , protocols::scoring::methods::pcs2::PcsInputCenterManager , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs2::PcsTensor , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs::PCS_data_input , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_data_input_Ts1 , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_Ts3 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_Ts4 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4 , protocols::topology_broker::ClaimerMessage
• operator== : protocols::id::AlignmentID , protocols::jd2::InnerJob , protocols::jd2::Job , protocols::sic_dock::Rose
• operator>> : protocols::abinitio::PairingStatEntry , protocols::abinitio::PairingStatistics , protocols::id::AlignmentID , protocols::jd2::archive::Batch , protocols::sasa_scores::Poly , protocols::sasa_scores::PPoly

- p -

• PClusterSet : protocols::pockets::PCluster
• PocketGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::PCluster , protocols::pockets::PClusterSet
• PointMutScanDriver : protocols::pmut_scan::Mutant , protocols::pmut_scan::MutationData
• protocols::jd2::JobDistributor : protocols::jd2::InnerJob
• protocols::jd2::JobDistributorFactory : protocols::jd2::archive::MPIArchiveJobDistributor
• protocols::jd2::JobInputter : protocols::jd2::InnerJob
• protocols::jd2::Parser : protocols::jd2::InnerJob

- t -

• TargetPocketGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid

- w -

• WorkUnitManager : protocols::wum::WorkUnitBase
• WorkUnitQueue : protocols::wum::WorkUnitBase
• WorkUnitQueue_Swapped : protocols::wum::WorkUnitManager