- j -

• j_ : protocols::frag_picker::Contact
• j_claim_ : protocols::environment::claims::VirtResClaim
• jacobian_ : protocols::kinematic_closure::ClosureSolution
• jd_master_rank_ : protocols::jd2::archive::ArchiveManager
• job_ : protocols::canonical_sampling::TemperingBase
• 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 , protocols::jd2::MSDJobDistributor
• job_inputter_creator_map_ : protocols::jd2::JobInputterFactory
• job_map_ : protocols::jd2::MSDJobDistributor
• job_outputter_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::jd2::JobDistributor , protocols::jd2::MSDJobDistributor
• job_outputter_creator_map_ : protocols::jd2::JobOutputterFactory
• job_type_text : protocols::boinc::BoincSharedMemory
• jobname_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• 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::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_id_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• 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::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::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::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_movers_ : protocols::protein_interface_design::movers::MapHotspot
• 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::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_pair_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup
• jump_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• jump_sample_ : protocols::abinitio::abscript::JumpSampleData , protocols::hybridization::FoldTreeHybridize , protocols::jumping::JumpSetup
• jump_set_ : protocols::matdes::OligomericAverageDegreeFilter
• jump_setup_ : protocols::topology_broker::MetalloClaimer
• jumpAtoms_ : protocols::jumping::ResiduePairJumpSingle
• jumpid_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• jumpnum_ : protocols::membrane::RotationMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover
• 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
• 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