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

- j -

• j() : protocols::farna::BasePairStep , protocols::frag_picker::Contact
• j_ : protocols::frag_picker::Contact
• j_claim_ : protocols::environment::claims::VirtResClaim
• j_next() : protocols::farna::BasePairStep
• jacobi() : protocols::evaluation::PCA
• jacobian_ : protocols::kinematic_closure::ClosureSolution
• 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
• 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::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MSDJobDistributor
• 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() : protocols::canonical_sampling::DbTrajectoryRecorder
• job_id_ : protocols::canonical_sampling::DbTrajectoryReader , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::trajectory::DbTrajectoryReader , protocols::trajectory::DbTrajectoryWriter
• job_id_end_ : protocols::jd2::MPIWorkPartitionJobDistributor
• job_id_start_ : protocols::jd2::MPIWorkPartitionJobDistributor
• job_inputter() : protocols::jd2::JobDistributor
• job_inputter_ : protocols::jd2::JobDistributor , protocols::jd2::MSDJobDistributor
• job_inputter_creator_map_ : protocols::jd2::JobInputterFactory
• job_inputter_input_source() : protocols::jd2::JobDistributor
• job_inputter_input_source_to_string() : protocols::jd2::JobInputter
• job_map_ : protocols::jd2::MSDJobDistributor
• job_outputter() : protocols::jd2::JobDistributor
• job_outputter_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::jd2::JobDistributor , protocols::jd2::MSDJobDistributor
• job_outputter_creator_map_ : protocols::jd2::JobOutputterFactory
• job_succeeded() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• job_succeeded_additional_output() : protocols::jd2::JobDistributor
• job_type_text : protocols::boinc::BoincSharedMemory
• JobCOP : protocols::dna::PDBOutput
• JobDataFeatures() : protocols::features::JobDataFeatures
• JobDataFeaturesCreator() : protocols::features::JobDataFeaturesCreator
• 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::MSDJobDistributor , 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 , protocols::mpi_refinement::MPI_Refinement
• JobOP : protocols::dna::PDBOutput
• JobOutputter() : protocols::jd2::JobOutputter
• JobOutputterCreator() : protocols::jd2::JobOutputterCreator
• JobOutputterFactory() : protocols::jd2::JobOutputterFactory
• JobOutputterMap : protocols::jd2::JobOutputterFactory
• JobOutputterObservers : protocols::jd2::Job
• 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::AtomTreeDiffJobDistributor , protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• join() : protocols::pockets::CClusterSet , protocols::pockets::PClusterSet
• join_two_poses_by_jump() : protocols::motif_grafting::movers::MotifGraftMover
• JointScore() : protocols::sic_dock::JointScore
• JointSequenceOperation() : protocols::toolbox::task_operations::JointSequenceOperation
• JScoreEvaluator() : protocols::simple_filters::JScoreEvaluator
• JScoreEvaluatorCreator() : protocols::simple_filters::JScoreEvaluatorCreator
• JSON_RPC() : protocols::rpc::JSON_RPC
• judge_facing() : protocols::features::strand_assembly::StrandBundleFeatures
• judge_sw_dis_too_close() : protocols::features::strand_assembly::StrandBundleFeatures
• judge_sw_inter_dis() : protocols::features::strand_assembly::StrandBundleFeatures
• judge_sw_torsion() : protocols::features::strand_assembly::StrandBundleFeatures
• jump() : protocols::environment::claims::VirtResClaim , protocols::farna::RNA_PairingTemplate
• Jump : protocols::forge::build::RelativeConnectRight
• jump : protocols::ligand_docking::Ligand_info , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::scoring::Interface , protocols::simple_filters::AlaScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::TaskAwareMinMover , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• jump_ : protocols::antibody::LHRepulsiveRamp , protocols::jumping::JumpSelector::JumpWeightDef , protocols::jumping::JumpSetup::JumpDef , 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::AlaScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::TaskAwareMinMover , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::toolbox::task_operations::ProteinCore , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• jump_active_ : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• jump_array_ : protocols::topology_broker::TMHTopologySamplerClaimer
• jump_atom() : protocols::topology_broker::claims::JumpClaim
• jump_atom1() : protocols::topology_broker::claims::JumpClaim
• jump_atom2() : protocols::topology_broker::claims::JumpClaim
• jump_atom_id_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• jump_atoms() : protocols::jumping::JumpSample
• jump_atoms_ : protocols::jumping::JumpSample
• jump_backward() : protocols::farna::RNA_PairingTemplate
• jump_backward_ : protocols::farna::RNA_PairingTemplate
• jump_change_frequency() : protocols::farna::RNA_DeNovoProtocol
• jump_change_frequency_ : protocols::farna::RNA_DeNovoProtocol
• jump_containing_helix() : protocols::nonlocal::HelixRotate
• jump_containing_sheet() : protocols::nonlocal::SheetTranslate
• jump_def() : protocols::topology_broker::FragmentJumpClaimer
• jump_def_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::FixTemplateJumpSetup , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::LoopJumpFoldCst , protocols::topology_broker::FragmentJumpClaimer
• jump_dir_ : protocols::rigid::RigidBodyDofTransMover
• jump_filters_ : protocols::protein_interface_design::movers::MapHotspot
• jump_forward() : protocols::farna::RNA_PairingTemplate
• jump_forward_ : protocols::farna::RNA_PairingTemplate
• jump_frags_ : protocols::hybridization::FoldTreeHybridize
• jump_id() : protocols::docking::DockingEnsemble , protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Transform_info , protocols::ligand_docking::Translate_info , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::scoring::Interface , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter
• jump_id_ : protocols::docking::DockingEnsemble , protocols::ligand_docking::RigidSearchMover , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter
• jump_library_file_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• jump_move_ : protocols::hybridization::HybridizeProtocol
• jump_move_repeat_ : protocols::hybridization::HybridizeProtocol
• jump_mover() : protocols::abinitio::KinematicControl
• jump_mover_ : protocols::abinitio::KinematicControl
• jump_movers_ : protocols::protein_interface_design::movers::MapHotspot
• jump_num() : protocols::matdes::SymUnsatHbondFilter
• jump_num_ : protocols::docking::membrane::MPDockingMover , protocols::matdes::SymUnsatHbondFilter , protocols::membrane::FlipMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::TryRotamers , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::TerminusDistanceFilter
• jump_number() : protocols::rigid::UniformRigidBodyMover
• jump_number_ : protocols::hybridization::ChunkTrialMover , protocols::hybridization::InsertChunkMover , protocols::scoring::Interface
• jump_numbers_ : protocols::farna::MultipleDomainMover
• jump_nums_ : protocols::toolbox::task_operations::SelectBySASAOperation
• jump_pairings_ : protocols::jumping::JumpSample
• jump_partners_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• Jump_point() : protocols::stepwise::modeler::rna::Jump_point
• jump_point_pair_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• jump_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• jump_sample() : protocols::abinitio::abscript::JumpSampleData
• jump_sample_ : protocols::abinitio::abscript::JumpSampleData , protocols::hybridization::FoldTreeHybridize , protocols::jumping::JumpSetup
• jump_set() : protocols::matdes::OligomericAverageDegreeFilter
• jump_set_ : protocols::matdes::OligomericAverageDegreeFilter
• jump_setup_ : protocols::topology_broker::MetalloClaimer
• jumpAtoms() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• jumpAtoms_ : protocols::jumping::ResiduePairJumpSingle
• jumpAtoms_defined() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• JumpCalculator() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• JumpCalculatorOP : protocols::topology_broker::RigidChunkClaimer
• JumpClaim() : protocols::environment::claims::JumpClaim , protocols::topology_broker::claims::JumpClaim
• JumpDataMap : protocols::environment::EnvClaimBroker
• JumpDef() : protocols::jumping::JumpSetup::JumpDef , protocols::jumping::ResiduePairJumpSetup::JumpDef
• JumpElement() : protocols::environment::claims::JumpElement
• JumpElemVect : protocols::environment::EnvClaimBroker
• JumpEvaluator() : protocols::simple_filters::JumpEvaluator
• jumpid_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• JumpingFoldConstraintsWrapper() : protocols::abinitio::JumpingFoldConstraintsWrapper
• JumpList : protocols::jumping::JumpSelector , protocols::rigid::RigidBodyPerturbNoCenterMover
• JumpNrEvaluator() : protocols::simple_filters::JumpNrEvaluator
• JumpNrEvaluatorCreator() : protocols::simple_filters::JumpNrEvaluatorCreator
• jumpnum_ : protocols::membrane::RotationMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover
• JumpNumber : protocols::environment::CoMTrackerCM , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover
• JumpOutMover() : protocols::moves::JumpOutMover
• JumpRotamerSidechainMover() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover
• jumps() : protocols::jumping::JumpSample , protocols::simple_filters::InterfaceSasaFilter
• jumps2pairings() : protocols::jumping::JumpSample
• jumps_ : protocols::jumping::JumpSample , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::JumpsFromAllPairings , protocols::jumping::ResiduePairJumpSetup , protocols::ligand_docking::SlideTogether , protocols::rbsegment_relax::AutoRBMover , protocols::simple_filters::InterfaceSasaFilter , protocols::stepwise::sampler::JumpStepWiseSampler
• jumps_and_cuts_from_foldtree() : protocols::hybridization::HybridizeFoldtreeDynamic
• JumpSample() : protocols::jumping::JumpSample
• JumpSampleData() : protocols::abinitio::abscript::JumpSampleData
• JumpSelector() : protocols::jumping::JumpSelector
• JumpSetup() : protocols::jumping::JumpSetup
• JumpsFromAllPairings() : protocols::jumping::JumpsFromAllPairings
• JumpStepWiseSampler() : protocols::stepwise::sampler::JumpStepWiseSampler
• JumpWeightDef() : protocols::jumping::JumpSelector::JumpWeightDef
• just_do_closure_check_ : protocols::stepwise::screener::RNA_ChainClosureScreener
• just_min_after_mutation_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• just_min_after_mutation_frequency_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• just_polar_hydrogens_ : protocols::simple_moves::ConstrainToIdealMover
• just_rna_backbone_ : protocols::simple_moves::ConstrainToIdealMover
• just_smooth_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• just_smooth_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio