- j -

• j_ : protocols::frag_picker::Contact , protocols::loop_modeling::loggers::Logger
• J_ : protocols::loop_modeling::loggers::Logger
• jacobian_ : protocols::kinematic_closure::ClosureSolution
• jd_master_rank_ : protocols::jd2::archive::ArchiveManager
• job_ : protocols::canonical_sampling::TemperatureController
• job_data_features_ : protocols::features::ProteinSilentReport
• job_dist_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• 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_creator_map_ : protocols::jd2::JobInputterFactory
• job_outputter_ : protocols::jd2::JobDistributor
• job_outputter_creator_map_ : protocols::jd2::JobOutputterFactory
• job_parameters_ : protocols::stepwise::sampling::protein::StepWisePoseSetup , protocols::stepwise::sampling::protein::StepWiseProteinBackboneSampler , protocols::stepwise::sampling::protein::StepWiseProteinModeler , protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler , protocols::stepwise::sampling::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler , protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler , protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup , protocols::stepwise::sampling::rna::legacy::StepWiseRNA_PoseSetup , protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler , protocols::stepwise::sampling::rna::StepWiseRNA_Clusterer , protocols::stepwise::sampling::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer , protocols::stepwise::sampling::rna::StepWiseRNA_Modeler , protocols::stepwise::sampling::rna::StepWiseRNA_PoseSelection , protocols::stepwise::sampling::rna::StepWiseRNA_ResidueSampler , protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD , protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator , protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler , protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList , protocols::stepwise::screener::NativeRMSD_Screener , protocols::stepwise::screener::PoseSelectionScreener
• job_parameters_exist_ : protocols::stepwise::sampling::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_ : 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::rotamer_sampler::rigid_body::RigidBodyRotamer , 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_atom_id_ : protocols::rotamer_sampler::rigid_body::RigidBodyRotamer
• jump_atoms_ : protocols::jumping::JumpSample
• jump_backward_ : protocols::farna::RNA_PairingTemplate
• jump_change_frequency_ : protocols::farna::RNA_DeNovoProtocol
• jump_def_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::FixTemplateJumpSetup , protocols::abinitio::JumpingFoldConstraints , 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_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_label_ : protocols::environment::claims::VirtResClaim
• 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_movers_ : protocols::protein_interface_design::movers::MapHotspot
• jump_nr_ : protocols::simple_filters::JumpEvaluator
• jump_num_ : 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::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::sampling::protein::StepWisePoseSetup , protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
• jump_point_pair_list_ : protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
• jump_res_ : protocols::stepwise::sampling::protein::StepWisePoseSetup
• jump_sample_ : protocols::abinitio::abscript::JumpSampleData , protocols::hybridization::FoldTreeHybridize , protocols::jumping::JumpSetup
• jump_setup_ : protocols::topology_broker::MetalloClaimer
• jumpAtoms_ : protocols::jumping::ResiduePairJumpSingle
• jumpid_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• 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::rotamer_sampler::JumpRotamer , protocols::simple_filters::InterfaceSasaFilter , protocols::stepwise::sampling::protein::StepWiseBetaAntiParallelJumpSampleGenerator
• just_do_closure_check_ : protocols::stepwise::screener::ChainClosureScreener
• just_min_after_mutation_frequency_ : protocols::stepwise::monte_carlo::rna::StepWiseMonteCarloOptions
• just_preminimize_ : protocols::stepwise::monte_carlo::rna::StepWiseMonteCarlo
• just_smooth_cycles_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio