Here is a list of all class members with links to the classes they belong to:

- j -

• j() : protocols::frag_picker::Contact
• j_ : protocols::frag_picker::Contact
• jacobi() : protocols::frag_picker::scores::RDCScore , protocols::evaluation::PCA
• Jcomputed() : core::scoring::RDC
• JCoupling() : protocols::frag_picker::scores::JCoupling
• JCouplingIO() : protocols::frag_picker::JCouplingIO
• jd2_signal_handler() : protocols::jd2::JobDistributor
• JD2ResourceManager() : protocols::jd2::JD2ResourceManager
• JD2ResourceManagerCreator : protocols::jd2::JD2ResourceManager
• JD2ResourceManagerJobInputter() : protocols::jd2::JD2ResourceManagerJobInputter
• jd_master_rank_ : protocols::jd2::archive::ArchiveManager
• Jdipolar() : core::scoring::RDC_Rohl , core::scoring::RDC
• Jdipolar_ : core::scoring::RDC , core::scoring::RDC_Rohl
• Jdipolar_computed_ : core::scoring::RDC
• JJH_Minimizer() : core::optimization::JJH_Minimizer
• jname2components_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• jname2subunits_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• jnum : core::kinematics::Node
• jnum2dofname_ : core::conformation::symmetry::SymmetryInfo
• Job() : protocols::jd2::Job
• job_ : protocols::canonical_sampling::TemperingBase
• job_data_features_ : protocols::features::ProteinSilentReport
• job_dist_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• job_failed() : protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::BOINCJobDistributor
• job_has_completed() : protocols::enzdes::EnzdesJobOutputter , protocols::features::DatabaseJobOutputter , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter , protocols::jd2::PDBJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter
• job_id_end_ : protocols::jd2::MPIWorkPartitionJobDistributor
• job_id_start_ : protocols::jd2::MPIWorkPartitionJobDistributor
• job_inputter() : protocols::jd2::JobDistributor
• job_inputter_ : protocols::jd2::JobDistributor
• job_inputter_creator_map_ : protocols::jd2::JobInputterFactory
• job_inputter_input_source() : protocols::jd2::JobDistributor
• job_inputter_input_source_to_string() : protocols::jd2::JobInputter
• job_outputter() : protocols::jd2::JobDistributor
• job_outputter_ : protocols::jd2::JobDistributor
• job_outputter_creator_map_ : protocols::jd2::JobOutputterFactory
• job_parameters() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• job_parameters_ : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWisePoseSetup , protocols::swa::protein::StepWiseProteinScreener , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_BaseCentroidScreener , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::rna::StepWiseRNA_Minimizer
• job_parameters_exist_ : protocols::swa::rna::StepWiseRNA_Clusterer
• job_succeeded() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• job_type_text : protocols::boinc::BoincSharedMemory
• JobCOP : protocols::dna::PDBOutput
• JobDataFeatures() : protocols::features::JobDataFeatures
• JobDataFeaturesCreator() : protocols::features::JobDataFeaturesCreator
• JOBDIST_OUTPUT_TAG : core::pose::datacache::CacheableDataType
• JobDistributor() : protocols::jd2::JobDistributor
• 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
• JobInputterCreator() : protocols::jd2::JobInputterCreator
• JobInputterFactory() : protocols::jd2::JobInputterFactory
• JobInputterMap : protocols::jd2::JobInputterFactory
• JobInputterRegistrator() : protocols::jd2::JobInputterRegistrator< T >
• jobname_ : protocols::loophash::MPI_LoopHashRefine
• JobOutputter() : protocols::jd2::JobOutputter
• JobOutputterCreator() : protocols::jd2::JobOutputterCreator
• JobOutputterFactory() : protocols::jd2::JobOutputterFactory
• JobOutputterMap : protocols::jd2::JobOutputterFactory
• JobOutputterRegistrator() : protocols::jd2::JobOutputterRegistrator< T >
• jobs_ : protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor
• jobs_assigned_ : protocols::jd2::MPIFileBufJobDistributor
• jobs_completed() : protocols::jd2::archive::ArchiveManager
• jobs_completed_ : protocols::jd2::archive::ArchiveManager
• jobs_returned_ : protocols::jd2::MPIFileBufJobDistributor
• JobVector : protocols::jobdist::BaseJobDistributor , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• join() : protocols::pockets::PClusterSet
• JointScore() : protocols::sic_dock::JointScore
• JointSequenceOperation() : protocols::toolbox::task_operations::JointSequenceOperation
• JScoreEvaluator() : protocols::simple_filters::JScoreEvaluator
• JScoreEvaluatorCreator() : protocols::simple_filters::JScoreEvaluatorCreator
• jump : protocols::ligand_docking::Ligand_info , core::conformation::Conformation , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pose::Pose , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::rna::RNA_PairingTemplate , protocols::scoring::Interface , protocols::simple_filters::AlaScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_moves::TaskAwareMinMover , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• JUMP : protocols::topology_broker::DofClaim
• Jump : core::conformation::Conformation , protocols::forge::build::RelativeConnectRight , core::kinematics::Jump
• jump_ : core::kinematics::tree::JumpAtom , core::pack::annealer::SimAnnealerBase , protocols::antibody2::LHRepulsiveRamp , protocols::jumping::JumpSetup::JumpDef , protocols::simple_filters::AlaScan , protocols::jumping::JumpSelector::JumpWeightDef , protocols::jumping::ResiduePairJumpSetup::JumpDef , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::SetAtomTree , protocols::seeded_abinitio::CoordinateCst , protocols::simple_filters::DeltaFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_moves::TaskAwareMinMover , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::ProteinCore , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• jump_active_ : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• jump_atom() : protocols::topology_broker::JumpClaim
• jump_atom_id() : core::conformation::Conformation
• jump_atoms() : protocols::jumping::JumpSample
• jump_atoms_ : protocols::jumping::JumpSample
• jump_backward() : protocols::rna::RNA_PairingTemplate
• jump_backward_ : protocols::rna::RNA_PairingTemplate
• jump_change_frequency() : protocols::rna::RNA_DeNovoProtocol
• jump_change_frequency_ : protocols::rna::RNA_DeNovoProtocol
• jump_clone_wts_ : core::conformation::symmetry::SymmetryInfo
• jump_clones() : core::conformation::symmetry::SymmetryInfo
• jump_clones_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• jump_containing_helix() : protocols::nonlocal::HelixRotate
• jump_containing_sheet() : protocols::nonlocal::SheetTranslate
• jump_cycles() : protocols::abinitio::JumpingFoldConstraints
• jump_def() : protocols::topology_broker::JumpClaimer
• jump_def_ : protocols::abinitio::FixTemplateJumpSetup , protocols::abinitio::AbrelaxApplication , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::LoopJumpFoldCst , protocols::topology_broker::JumpClaimer
• jump_dir_ : core::conformation::symmetry::SymDof , protocols::rigid::RigidBodyDofTransMover
• jump_direction() : core::conformation::symmetry::SymDof
• jump_edge() : core::kinematics::FoldTree
• jump_edge_ : core::kinematics::FoldTree
• jump_edge_count : core::kinematics::FoldTree
• jump_exists() : core::kinematics::FoldTree
• jump_filters_ : protocols::protein_interface_design::movers::MapHotspot
• jump_follows() : core::conformation::symmetry::SymmetryInfo
• jump_follows_ : core::conformation::symmetry::SymmetryInfo
• jump_forward() : protocols::rna::RNA_PairingTemplate
• jump_forward_ : protocols::rna::RNA_PairingTemplate
• jump_frags_ : protocols::hybridization::FoldTreeHybridize , protocols::abinitio::JumpingFoldConstraints
• jump_id : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Transform_info , protocols::ligand_docking::Translate_info , protocols::scoring::Interface , protocols::simple_filters::ShapeComplementarityFilter , protocols::docking::DockingEnsemble
• jump_id_ : protocols::docking::DockingEnsemble , protocols::simple_filters::ShapeComplementarityFilter , protocols::ligand_docking::RigidSearchMover
• jump_id_begin() : core::kinematics::MoveMap
• jump_id_end() : core::kinematics::MoveMap
• jump_id_map_ : core::kinematics::MoveMap
• jump_is_independent() : core::conformation::symmetry::SymmetryInfo
• jump_library_file_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• jump_mover() : protocols::abinitio::KinematicControl
• jump_mover_ : protocols::abinitio::KinematicControl
• jump_movers_ : protocols::protein_interface_design::movers::MapHotspot
• jump_nr() : core::kinematics::FoldTree
• jump_nr_ : protocols::simple_filters::JumpEvaluator
• jump_num_ : protocols::simple_filters::BuriedUnsatHbondFilter , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::SpinMover , protocols::simple_filters::TerminusDistanceFilter
• jump_number_ : protocols::hybridization::ChunkTrialMover , protocols::hybridization::InsertChunkMover , protocols::scoring::Interface
• jump_numbers_ : protocols::rna::MultipleDomainMover
• jump_nums_ : protocols::toolbox::task_operations::SelectBySASAOperation
• jump_pairings_ : protocols::jumping::JumpSample
• jump_partners_ : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• jump_point() : core::kinematics::FoldTree
• Jump_point() : protocols::swa::rna::Jump_point
• jump_point_ : core::kinematics::FoldTree
• jump_point_pair_list_ : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• jump_res_ : core::kinematics::ShortestPathInFoldTree , protocols::swa::StepWisePoseSetup
• jump_sample_ : protocols::jumping::JumpSetup , protocols::hybridization::FoldTreeHybridize
• jump_setup_ : protocols::topology_broker::MetalloClaimer
• jump_string_to_jump_num_ : core::conformation::symmetry::SymmData
• jump_string_to_virtual_pair_ : core::conformation::symmetry::SymmData
• jumpAtoms() : protocols::jumping::ResiduePairJumpSingle , protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• jumpAtoms_ : protocols::jumping::ResiduePairJumpSingle
• jumpAtoms_defined() : protocols::jumping::ResiduePairJumpSingle , protocols::jumping::ResiduePairJump
• JumpCalculator() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• JumpCalculatorOP : protocols::topology_broker::RigidChunkClaimer
• JumpClaim() : protocols::topology_broker::JumpClaim
• JumpClaimer() : protocols::topology_broker::JumpClaimer
• JumpDef() : protocols::jumping::JumpSetup::JumpDef , protocols::jumping::ResiduePairJumpSetup::JumpDef
• JumpEvaluator() : protocols::simple_filters::JumpEvaluator
• jumpfrom : core::kinematics::Node
• JumpID() : core::id::JumpID
• jumpid_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• JumpID_Map : core::kinematics::MoveMap
• JumpingFoldConstraints() : protocols::abinitio::JumpingFoldConstraints
• JumpingFoldConstraintsWrapper() : protocols::abinitio::JumpingFoldConstraintsWrapper
• JumpingFrame() : core::fragment::JumpingFrame
• JumpList : protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::jumping::JumpSelector
• jumpmark : core::kinematics::Node
• JumpNrEvaluator() : protocols::simple_filters::JumpNrEvaluator
• JumpNrEvaluatorCreator() : protocols::simple_filters::JumpNrEvaluatorCreator
• JumpOutMover() : protocols::moves::JumpOutMover
• JumpRotamerSidechainMover() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover
• jumps() : protocols::jumping::JumpSample , protocols::simple_filters::InterfaceSasaFilter
• jumps2pairings() : protocols::jumping::JumpSample
• jumps_ : core::io::silent::BinaryProteinSilentStruct , protocols::simple_filters::InterfaceSasaFilter , protocols::swa::protein::StepWiseProteinJumpSampleGenerator , protocols::swa::protein::StepWiseBetaAntiParallelJumpSampleGenerator , core::io::silent::RNA_SilentStruct , protocols::jumping::JumpSetup , protocols::rbsegment_relax::AutoRBMover , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::JumpsFromAllPairings , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::ligand_docking::SlideTogether , protocols::jumping::JumpSample , protocols::jumping::JumpSelector , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::BinaryRNASilentStruct
• jumps_and_cuts_from_foldtree() : protocols::hybridization::HybridizeFoldtreeDynamic
• JumpSample() : protocols::jumping::JumpSample
• JumpSelector() : protocols::jumping::JumpSelector
• JumpSetup() : protocols::jumping::JumpSetup
• JumpsFromAllPairings() : protocols::jumping::JumpsFromAllPairings
• jumpto : core::kinematics::Node
• JumpWeightDef() : protocols::jumping::JumpSelector::JumpWeightDef
• junction_residue_array_ : protocols::swa::protein::StepWiseProteinPoseSetup
• just_output_score_ : protocols::swa::rna::RNA_LoopCloseSampler
• just_smooth_cycles() : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler
• just_smooth_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio