- j -

• j : core::scoring::fiber_diffraction::Hankel
• J_ : core::io::nmr::ParaIon
• j_ : core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator , protocols::frag_picker::Contact
• j_claim_ : protocols::environment::claims::VirtResClaim
• jacobian_ : protocols::kinematic_closure::ClosureSolution
• jacobian_chain_ : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• jacobian_sampler_ : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• jd_master_rank_ : protocols::jd2::archive::ArchiveManager
• jd_output_suffix_ : protocols::jd3::output::OutputSpecification
• Jdipolar_ : core::scoring::RDC , core::scoring::RDC_Rohl
• Jdipolar_computed_ : core::scoring::RDC
• 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_dag_ : protocols::jd3::job_distributors::JobExtractor , protocols::jd3::job_distributors::VanillaJobDistributor
• job_data_ : core::chemical::sdf::MolWriter
• job_data_features_ : protocols::features::ProteinSilentReport
• job_definition_file_tags_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• job_digraph_ : protocols::jd3::JobDigraphUpdater
• job_dist_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• job_edge_pool_ : protocols::jd3::JobDigraph
• job_genealogist_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• job_graph_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen
• job_id_ : protocols::canonical_sampling::DbTrajectoryRecorder , protocols::trajectory::DbTrajectoryReader , protocols::trajectory::DbTrajectoryWriter
• job_index_ : protocols::jd3::LarvalJob
• job_indices_seen_ : protocols::jd3::job_distributors::JobExtractor
• job_inputter_ : protocols::jd2::JobDistributor , protocols::jd2::JobsContainer , protocols::jd2::VectorPoseJobDistributor
• job_inputter_creator_map_ : protocols::jd2::JobInputterFactory
• job_map_ : protocols::jd2::VectorPoseJobDistributor
• job_me_ : protocols::chemically_conjugated_docking::UBQ_GTPaseMover
• job_node_ : protocols::jd3::InnerLarvalJob
• job_nodes_for_dag_node_ : protocols::jd3::JobGenealogist
• job_offset_ : protocols::jd3::dag_node_managers::NodeManager
• job_options : protocols::jd3::chunk_library::ChunkLibraryPreliminaryLarvalJob , protocols::jd3::full_model::FullModelPreliminaryLarvalJob , protocols::jd3::standard::PreliminaryLarvalJob
• job_outputter_ : protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::jd2::JobDistributor , protocols::jd2::VectorPoseJobDistributor
• job_outputter_creator_map_ : protocols::jd2::JobOutputterFactory
• job_queen_ : protocols::jd3::job_distributors::JobExtractor , protocols::jd3::job_distributors::VanillaJobDistributor
• job_results : protocols::jd3::CompletedJobOutput
• job_results_ : protocols::jd3::job_distributors::VanillaJobDistributor
• job_results_have_been_discarded_for_stage_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• job_results_that_should_be_discarded_ : protocols::jd3::dag_node_managers::NodeManager
• job_tag : protocols::jd3::chunk_library::ChunkLibraryPreliminaryLarvalJob , protocols::jd3::full_model::FullModelPreliminaryLarvalJob , protocols::jd3::standard::PreliminaryLarvalJob
• job_tag_ : core::simple_metrics::composite_metrics::ProtocolSettingsMetric , protocols::jd3::InnerLarvalJob
• job_tracker_ : protocols::jd3::JobQueen
• job_type_text : protocols::boinc::BoincSharedMemory
• jobdef_tag_ : protocols::jd3::InnerLarvalJob
• jobindex_on_originating_node_ : protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary , protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase
• joblist_ : protocols::jd2::JobsContainer
• jobname_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• JobQueen : protocols::jd3::JQKey
• jobs_ : protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor
• jobs_assigned_ : protocols::jd2::MPIFileBufJobDistributor
• jobs_completed_ : protocols::jd2::archive::ArchiveManager
• jobs_for_current_digraph_node_ : protocols::jd3::job_distributors::JobExtractor
• jobs_returned_ : protocols::jd2::MPIFileBufJobDistributor
• jobs_running_for_digraph_nodes_ : protocols::jd3::job_distributors::JobExtractor
• jump : protocols::denovo_design::movers::CutAndJump , protocols::ligand_docking::Ligand_info
• jump_ : core::kinematics::tree::JumpAtom , core::pack::annealer::SimAnnealerBase , core::select::jump_selector::JumpIndexSelector , core::select::residue_selector::JumpDownstreamSelector , core::select::residue_selector::JumpUpstreamSelector , protocols::antibody::LHRepulsiveRamp , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::docking::SlideIntoContact , protocols::jumping::JumpSelector::JumpWeightDef , protocols::jumping::JumpSetup::JumpDef , protocols::jumping::ResiduePairJumpSetup::JumpDef , protocols::membrane::SpinAroundPartnerMover , protocols::membrane::TransformIntoMembraneMover , protocols::minimization_packing::TaskAwareMinMover , 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_ddg::AlaScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::InterfaceHbondsFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::task_operations::ProteinCore , protocols::task_operations::ProteinInterfaceDesignOperation
• jump_actions_ : core::select::movemap::MoveMapFactory
• jump_active_ : protocols::task_operations::RestrictToInterfaceVectorOperation
• jump_array_ : protocols::topology_broker::TMHTopologySamplerClaimer
• jump_atom_id_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• jump_atoms_ : protocols::jumping::JumpSample
• jump_backward_ : core::import_pose::libraries::RNA_PairingTemplate
• jump_change_frequency_ : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::rna::denovo::movers::RNA_DeNovoMasterMover
• jump_clone_wts_ : core::conformation::symmetry::SymmetryInfo
• jump_clones_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• jump_dbase_fname_ : protocols::splice::RBOutMover
• jump_def_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::FixTemplateJumpSetup , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::LoopJumpFoldCst , protocols::topology_broker::FragmentJumpClaimer
• jump_dir_ : core::conformation::symmetry::SymDof , protocols::rigid::RigidBodyDofTransMover
• jump_edge_ : core::kinematics::FoldTree
• jump_edge_count : core::kinematics::FoldTree
• jump_end_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• jump_filters_ : protocols::protein_interface_design::movers::MapHotspot
• jump_follows_ : core::conformation::symmetry::SymmetryInfo
• jump_forward_ : core::import_pose::libraries::RNA_PairingTemplate
• jump_frags_ : protocols::hybridization::FoldTreeHybridize
• jump_from_foldtree_ : protocols::splice::RBOutMover
• jump_histogram_ : protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter
• jump_histogram_bin_width_ : protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter
• jump_histogram_binwidth_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• jump_histogram_binwidth_rotvector_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• jump_histogram_boxsize_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• jump_histogram_max_ : protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter
• jump_histogram_min_ : protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter
• jump_id_ : core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric , protocols::docking::DockingEnsemble , protocols::ligand_docking::RigidSearchMover , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter
• jump_id_map_ : core::kinematics::MoveMap
• jump_ids_ : protocols::features::InterfaceDdGMover
• jump_is_mirrored_ : core::conformation::symmetry::MirrorSymmetricConformation
• jump_label_to_number_ : core::environment::SequenceAnnotation
• jump_library_ : protocols::splice::RBInMover
• jump_library_file_ : core::import_pose::options::RNA_FragmentMonteCarloOptions
• jump_library_filename_ : core::import_pose::libraries::RNA_JumpLibrary
• jump_move_ : protocols::hybridization::HybridizeProtocol
• jump_move_repeat_ : protocols::hybridization::HybridizeProtocol
• jump_mover_ : protocols::abinitio::KinematicControl
• jump_movers_ : protocols::protein_interface_design::movers::MapHotspot
• jump_neighbors_ : core::environment::FoldTreeSketch::Node
• jump_num_ : protocols::docking::membrane::MPDockingMover , protocols::matdes::SymUnsatHbondFilter , protocols::membrane::FlipMover , protocols::membrane::TiltMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::TryRotamers , protocols::recces::sampler::rna::MC_RNA_OneJump , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::TerminusDistanceFilter
• jump_number_ : protocols::hybridization::ChunkTrialMover , protocols::hybridization::InsertChunkMover , protocols::scoring::Interface
• jump_numbers_ : protocols::rna::denovo::coarse::MultipleDomainMover
• jump_nums_ : protocols::hbnet::HBNetStapleInterface , protocols::task_operations::SelectBySASAOperation
• jump_pairings_ : protocols::jumping::JumpSample
• jump_partners_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• jump_point_ : core::kinematics::FoldTree
• jump_point_pair_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• jump_res_ : core::import_pose::FullModelPoseBuilder , core::kinematics::ShortestPathInFoldTree , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• jump_resnum_and_chain_ : core::scoring::rna::RNA_StubCoordinateEnergy
• jump_sample_ : protocols::abinitio::abscript::JumpSampleData , protocols::hybridization::FoldTreeHybridize , protocols::jumping::JumpSetup
• jump_set_ : protocols::matdes::OligomericAverageDegreeFilter
• jump_setup_ : protocols::topology_broker::MetalloClaimer
• jump_start_ : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• jump_string_to_jump_num_ : core::conformation::symmetry::SymmData
• jump_string_to_virtual_pair_ : core::conformation::symmetry::SymmData
• jumpAtoms_ : protocols::jumping::ResiduePairJumpSingle
• jumpfrom : core::kinematics::Node
• jumpid_ : protocols::loop_grower::SheetPositions , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• jumpmark : core::kinematics::Node
• jumpnum_ : protocols::membrane::RotationMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover
• jumps_ : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreJumpFileSilentStruct , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::jumping::JumpSample , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::JumpsFromAllPairings , protocols::jumping::ResiduePairJumpSetup , protocols::rbsegment_relax::AutoRBMover , protocols::simple_filters::InterfaceSasaFilter , protocols::stepwise::sampler::jump::JumpStepWiseSampler
• jumps_info_ : core::pose::copydofs::CopyDofsInfo
• jumpto : core::kinematics::Node
• junction_failure_set_ : protocols::pose_creation::MakeJunctionsMover
• junction_rmsd_thresh_ : protocols::pose_creation::MakeJunctionsMover
• just_do_closure_check_ : protocols::stepwise::screener::RNA_ChainClosureScreener
• 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