- j -

• j() : core::pose::rna::BasePairStep , protocols::frag_picker::Contact
• j_next() : core::pose::rna::BasePairStep
• J_SB() : core::scoring::nmr::pre::PREMultiSet
• J_SBMF() : core::scoring::nmr::pre::PREMultiSet
• jacobi() : protocols::evaluation::PCA
• JacobianStructure() : core::kinematics::jacobian::JacobianStructure
• JacobiLoopClosureMover() : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• jagged_array() : protocols::mean_field::jagged_array< T, A >
• Jcomputed() : core::scoring::RDC
• JCoupling() : protocols::frag_picker::scores::JCoupling
• JCouplingIO() : protocols::frag_picker::JCouplingIO
• jd2_signal_handler() : protocols::jd2::JobDistributor
• jd_output_suffix() : protocols::jd3::output::MultipleOutputSpecification , protocols::jd3::output::OutputSpecification
• Jdipolar() : core::scoring::RDC , core::scoring::RDC_Rohl
• JGJobNode() : protocols::jd3::JGJobNode
• JGResultNode() : protocols::jd3::JGResultNode
• JJH_Minimizer() : core::optimization::JJH_Minimizer
• Job() : protocols::jd2::Job , protocols::jd3::Job
• job_available_on_command_line() : protocols::jd3::chunk_library_inputters::ChunkLibraryInputter , protocols::jd3::chunk_library_inputters::PDBChunkLibraryInputter , protocols::jd3::full_model_inputters::FullModelInputter , protocols::jd3::full_model_inputters::PDBFullModelInputter , protocols::jd3::full_model_inputters::SilentFileFullModelInputter , protocols::jd3::pose_inputters::PDBPoseInputter , protocols::jd3::pose_inputters::PoseInputter , protocols::jd3::pose_inputters::SilentFilePoseInputter
• job_dag() : protocols::jd3::JobDigraphUpdater
• job_dag_node() : protocols::jd3::JGJobNode
• job_def_complex_type_name() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• job_definition_xsd() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen , protocols::jd3::standard::StandardJobQueen
• job_failed() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor , protocols::jd2::VectorPoseJobDistributor
• job_has_already_completed() : protocols::jd3::pose_outputters::DeNovoSilentFilePoseOutputter , protocols::jd3::pose_outputters::PDBPoseOutputter , protocols::jd3::pose_outputters::PoseOutputter , protocols::jd3::pose_outputters::SecondaryPoseOutputter , protocols::jd3::pose_outputters::SilentFilePoseOutputter
• job_has_completed() : protocols::enzdes::EnzdesJobOutputter , protocols::features::DatabaseJobOutputter , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter , protocols::jd2::RNA_DeNovoJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jd2::wwPDBJobOutputter
• job_id() : protocols::canonical_sampling::DbTrajectoryRecorder
• job_index() : protocols::jd3::LarvalJob
• job_inputter() : protocols::jd2::JobDistributor
• job_inputter_input_source() : protocols::jd2::JobDistributor
• job_inputter_input_source_to_string() : protocols::jd2::JobInputter
• job_node() : protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob
• job_offset() : protocols::jd3::dag_node_managers::NodeManager
• job_outputter() : protocols::jd2::JobDistributor
• job_queue_empty() : protocols::jd3::job_distributors::JobExtractor
• job_result_id() : protocols::jd3::dag_node_managers::ResultElements
• job_results_that_should_be_discarded() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen , protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen
• job_subelement_mangler() : protocols::multistage_rosetta_scripts::MRSJobQueen
• 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_tag() : protocols::jd3::chunk_library::ChunkLibraryInnerLarvalJob , protocols::jd3::full_model::FullModelInnerLarvalJob , protocols::jd3::InnerLarvalJob , protocols::jd3::LarvalJob
• job_tag_with_index_suffix() : protocols::jd3::LarvalJob
• JobDataFeatures() : protocols::features::JobDataFeatures
• jobdef_tag() : protocols::jd3::InnerLarvalJob
• JobDigraph() : protocols::jd3::JobDigraph
• JobDigraphUpdater() : protocols::jd3::JobDigraphUpdater
• JobDirectedEdge() : protocols::jd3::JobDirectedEdge
• JobDirectedNode() : protocols::jd3::JobDirectedNode
• JobDistributor() : protocols::jd2::JobDistributor , protocols::jd3::JobDistributor
• JobExtractor() : protocols::jd3::job_distributors::JobExtractor
• JobGenealogist() : protocols::jd3::JobGenealogist
• jobindex_on_originating_node() : protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary , protocols::cyclic_peptide_predict::HierarchicalHybridJD_ResultsSummaryBase
• JobInputterCreator() : protocols::jd2::JobInputterCreator
• JobInputterFactory() : protocols::jd2::JobInputterFactory
• JobInputterRegistrator() : protocols::jd2::JobInputterRegistrator< T >
• JobOutputter() : protocols::jd2::JobOutputter
• JobOutputterCreator() : protocols::jd2::JobOutputterCreator
• JobOutputterFactory() : protocols::jd2::JobOutputterFactory
• JobOutputterRegistrator() : protocols::jd2::JobOutputterRegistrator< T >
• JobOutputWriter() : protocols::jd3::JobOutputWriter
• JobQueen() : protocols::jd3::JobQueen
• JobResult() : protocols::jd3::JobResult
• jobs_are_still_running() : protocols::jd3::dag_node_managers::NodeManager
• jobs_completed() : protocols::jd2::archive::ArchiveManager
• jobs_remain() : protocols::jd3::job_distributors::JobExtractor
• jobs_that_should_be_output() : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::JobQueen , protocols::jd3::standard::StandardJobQueen , protocols::multistage_rosetta_scripts::MRSJobQueen
• JobsContainer() : protocols::jd2::JobsContainer
• JobSummary() : protocols::jd3::JobSummary
• JobTracker() : protocols::jd3::JobTracker
• join() : protocols::pockets::CClusterSet , protocols::pockets::PClusterSet
• join_pieces() : protocols::fold_from_loops::utils::Nub
• join_two_poses_by_jump() : protocols::motif_grafting::movers::MotifGraftMover
• JointScore() : protocols::sic_dock::JointScore
• JointSequenceOperation() : protocols::task_operations::JointSequenceOperation
• JQKey() : protocols::jd3::JQKey
• 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() : core::conformation::Conformation , core::import_pose::libraries::RNA_PairingTemplate , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::kinematics::AtomTree
• Jump() : core::kinematics::Jump
• jump() : core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pose::Pose , core::select::jump_selector::JumpIndexSelector , protocols::environment::claims::VirtResClaim , protocols::minimization_packing::TaskAwareMinMover , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::scoring::Interface , protocols::simple_ddg::AlaScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::task_operations::ProteinInterfaceDesignOperation
• jump_atom() : protocols::topology_broker::claims::JumpClaim
• jump_atom1() : protocols::topology_broker::claims::JumpClaim
• jump_atom2() : protocols::topology_broker::claims::JumpClaim
• jump_atom_id() : core::conformation::Conformation
• jump_atoms() : protocols::jumping::JumpSample
• jump_backward() : core::import_pose::libraries::RNA_PairingTemplate
• jump_change_frequency() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• jump_clones() : core::conformation::symmetry::SymmetryInfo
• jump_containing_helix() : protocols::nonlocal::HelixRotate
• jump_containing_sheet() : protocols::nonlocal::SheetTranslate
• jump_dbase_fname() : protocols::splice::RBOutMover
• jump_def() : protocols::topology_broker::FragmentJumpClaimer
• jump_direction() : core::conformation::symmetry::SymDof
• jump_edge() : core::kinematics::FoldTree
• jump_exists() : core::kinematics::FoldTree
• jump_follows() : core::conformation::symmetry::SymmetryInfo
• jump_forward() : core::import_pose::libraries::RNA_PairingTemplate
• jump_from_foldtree() : protocols::splice::RBOutMover
• jump_histogram() : 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_id() : core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric , protocols::docking::DockingEnsemble , protocols::ligand_docking::Rotate_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_begin() : core::kinematics::MoveMap
• jump_id_end() : core::kinematics::MoveMap
• jump_ids() : protocols::ligand_docking::TransformEnsemble_info
• jump_is_independent() : core::conformation::symmetry::SymmetryInfo
• jump_library() : protocols::splice::RBInMover
• jump_library_file() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• jump_mover() : protocols::abinitio::KinematicControl
• jump_nr() : core::kinematics::FoldTree
• jump_num() : protocols::matdes::SymUnsatHbondFilter
• jump_number() : protocols::rigid::UniformRigidBodyMover
• jump_pairs() : core::pose::full_model_info::FullModelInfo
• jump_point() : core::kinematics::FoldTree
• Jump_point() : protocols::stepwise::modeler::rna::Jump_point
• jump_res_map() : core::pose::full_model_info::FullModelInfo
• jump_sample() : protocols::abinitio::abscript::JumpSampleData
• jump_selector_loader_ct_namer() : protocols::parser::JumpSelectorLoader
• jump_selector_xml_schema_group_name() : core::select::jump_selector::JumpSelectorFactory
• jump_set() : protocols::matdes::OligomericAverageDegreeFilter
• jumpAtoms() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• jumpAtoms_defined() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• JumpCalculator() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• JumpClaim() : protocols::environment::claims::JumpClaim , protocols::topology_broker::claims::JumpClaim
• JumpDef() : protocols::jumping::JumpSetup::JumpDef , protocols::jumping::ResiduePairJumpSetup::JumpDef
• JumpDownstreamSelector() : core::select::residue_selector::JumpDownstreamSelector
• JumpElement() : protocols::environment::claims::JumpElement
• JumpEvaluator() : protocols::simple_filters::JumpEvaluator
• JumpID() : core::id::JumpID
• JumpIndexSelector() : core::select::jump_selector::JumpIndexSelector
• JumpingFoldConstraintsWrapper() : protocols::abinitio::JumpingFoldConstraintsWrapper
• JumpingFrame() : core::fragment::JumpingFrame
• JumpMetric() : protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetric
• JumpNrEvaluator() : protocols::simple_filters::JumpNrEvaluator
• JumpNrEvaluatorCreator() : protocols::simple_filters::JumpNrEvaluatorCreator
• JumpOutMover() : protocols::moves::JumpOutMover
• JumpRotamerSidechainMover() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover
• jumps() : protocols::jumping::JumpSample , protocols::simple_filters::InterfaceSasaFilter
• jumps2pairings() : protocols::jumping::JumpSample
• jumps_and_cuts_from_foldtree() : protocols::hybridization::HybridizeFoldtreeDynamic
• jumps_info() : core::pose::copydofs::CopyDofsInfo
• JumpSample() : protocols::jumping::JumpSample
• JumpSampleData() : protocols::abinitio::abscript::JumpSampleData
• JumpSelector() : core::select::jump_selector::JumpSelector , protocols::jumping::JumpSelector
• JumpSelectorFactory() : core::select::jump_selector::JumpSelectorFactory
• JumpSelectorLoader() : protocols::parser::JumpSelectorLoader
• JumpSelectorRegistrator() : core::select::jump_selector::JumpSelectorRegistrator< T >
• JumpSetup() : protocols::jumping::JumpSetup
• JumpsFromAllPairings() : protocols::jumping::JumpsFromAllPairings
• JumpStepWiseSampler() : protocols::stepwise::sampler::jump::JumpStepWiseSampler
• JumpUpstreamSelector() : core::select::residue_selector::JumpUpstreamSelector
• JumpWeightDef() : protocols::jumping::JumpSelector::JumpWeightDef
• just_min_after_mutation_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• just_simple_cycles() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• just_smooth_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio