- j -

• j_ : protocols::frag_picker::Contact
• jd_master_rank_ : protocols::jd2::archive::ArchiveManager
• Jdipolar_ : core::scoring::RDC_Rohl , core::scoring::RDC
• 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_ : protocols::canonical_sampling::TemperingBase
• job_data_features_ : protocols::features::ProteinSilentReport
• job_dist_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• job_id_end_ : protocols::jd2::MPIWorkPartitionJobDistributor
• job_id_start_ : protocols::jd2::MPIWorkPartitionJobDistributor
• job_inputter_ : protocols::jd2::JobDistributor
• job_inputter_creator_map_ : protocols::jd2::JobInputterFactory
• job_outputter_ : protocols::jd2::JobDistributor
• job_outputter_creator_map_ : protocols::jd2::JobOutputterFactory
• job_parameters_ : 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 , protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWisePoseSetup
• job_parameters_exist_ : protocols::swa::rna::StepWiseRNA_Clusterer
• job_type_text : protocols::boinc::BoincSharedMemory
• jobname_ : protocols::loophash::MPI_LoopHashRefine
• jobs_ : protocols::jd2::JobDistributor , protocols::jobdist::BaseJobDistributor
• jobs_assigned_ : protocols::jd2::MPIFileBufJobDistributor
• jobs_completed_ : protocols::jd2::archive::ArchiveManager
• jobs_returned_ : protocols::jd2::MPIFileBufJobDistributor
• jump : protocols::ligand_docking::Ligand_info
• jump_ : core::kinematics::tree::JumpAtom , core::pack::annealer::SimAnnealerBase , protocols::antibody2::LHRepulsiveRamp , protocols::jumping::JumpSetup::JumpDef , 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::AlaScan , 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_atoms_ : protocols::jumping::JumpSample
• jump_backward_ : protocols::rna::RNA_PairingTemplate
• jump_change_frequency_ : protocols::rna::RNA_DeNovoProtocol
• jump_clone_wts_ : core::conformation::symmetry::SymmetryInfo
• jump_clones_ : core::conformation::symmetry::SymmetryInfo , core::conformation::symmetry::SymmData
• jump_def_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::LoopJumpFoldCst , protocols::abinitio::FixTemplateJumpSetup , protocols::topology_broker::JumpClaimer
• jump_dir_ : core::conformation::symmetry::SymDof , protocols::rigid::RigidBodyDofTransMover
• jump_edge_ : core::kinematics::FoldTree
• jump_edge_count : core::kinematics::FoldTree
• jump_filters_ : protocols::protein_interface_design::movers::MapHotspot
• jump_follows_ : core::conformation::symmetry::SymmetryInfo
• jump_forward_ : protocols::rna::RNA_PairingTemplate
• jump_frags_ : protocols::abinitio::JumpingFoldConstraints , protocols::hybridization::FoldTreeHybridize
• jump_id : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Transform_info , protocols::ligand_docking::Translate_info
• jump_id_ : protocols::docking::DockingEnsemble , protocols::ligand_docking::RigidSearchMover , protocols::simple_filters::ShapeComplementarityFilter
• jump_id_map_ : core::kinematics::MoveMap
• jump_library_file_ : protocols::rna::RNA_DeNovoProtocol , protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• jump_mover_ : protocols::abinitio::KinematicControl
• jump_movers_ : protocols::protein_interface_design::movers::MapHotspot
• jump_nr_ : protocols::simple_filters::JumpEvaluator
• jump_num_ : protocols::simple_filters::BuriedUnsatHbondFilter , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::TryRotamers , protocols::simple_filters::TerminusDistanceFilter
• jump_number_ : protocols::scoring::Interface , protocols::hybridization::ChunkTrialMover , protocols::hybridization::InsertChunkMover
• 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_pair_list_ : protocols::swa::rna::StepWiseRNA_JobParameters_Setup
• jump_res_ : core::kinematics::ShortestPathInFoldTree , protocols::swa::StepWisePoseSetup
• jump_sample_ : protocols::hybridization::FoldTreeHybridize , protocols::jumping::JumpSetup
• 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
• jumpfrom : core::kinematics::Node
• jumpid_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• jumpmark : core::kinematics::Node
• jumps_ : protocols::jumping::JumpSelector , protocols::swa::protein::StepWiseProteinJumpSampleGenerator , protocols::simple_filters::InterfaceSasaFilter , protocols::jumping::JumpSample , protocols::jumping::JumpSetup , protocols::rbsegment_relax::AutoRBMover , protocols::swa::protein::StepWiseProteinResidueSampler , protocols::jumping::ResiduePairJumpSetup , core::io::silent::BinaryProteinSilentStruct , protocols::ligand_docking::SlideTogether , core::io::silent::RNA_SilentStruct , protocols::swa::protein::StepWiseBetaAntiParallelJumpSampleGenerator , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::BinaryRNASilentStruct , protocols::jumping::JumpsFromAllPairings
• jumpto : core::kinematics::Node
• junction_residue_array_ : protocols::swa::protein::StepWiseProteinPoseSetup
• just_output_score_ : protocols::swa::rna::RNA_LoopCloseSampler
• just_smooth_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio