Here is a list of all namespace members with links to the namespace documentation for each member:

- j -

• jacobi() : core::scoring , protocols::toolbox
• jacobi3() : core::scoring , protocols::cluster::calibur
• JacobianStructureCOP : core::kinematics::jacobian
• JacobianStructureOP : core::kinematics::jacobian
• JacobiLoopClosureMoverCOP : protocols::loops::loop_closure::jacobi
• JacobiLoopClosureMoverOP : protocols::loops::loop_closure::jacobi
• jagged_array_bool : protocols::mean_field
• jagged_array_char : protocols::mean_field
• jagged_array_double : protocols::mean_field
• jagged_array_float : protocols::mean_field
• jagged_array_int : protocols::mean_field
• jagged_array_long : protocols::mean_field
• jagged_array_longdouble : protocols::mean_field
• jagged_array_schar : protocols::mean_field
• jagged_array_short : protocols::mean_field
• jagged_array_size : protocols::mean_field
• jagged_array_size_t : protocols::mean_field
• jagged_array_ssize : protocols::mean_field
• jagged_array_ssize_t : protocols::mean_field
• jagged_array_uchar : protocols::mean_field
• jagged_array_uint : protocols::mean_field
• jagged_array_ulong : protocols::mean_field
• jagged_array_ushort : protocols::mean_field
• JD2_BOGUS_JOB : protocols::jd2
• jd2_used() : protocols::jd2
• jd3_job_previously_executed : protocols::jd3
• jd3_job_status_failed_do_not_retry : protocols::jd3
• jd3_job_status_failed_max_retries : protocols::jd3
• jd3_job_status_failed_retry : protocols::jd3
• jd3_job_status_failed_w_exception : protocols::jd3
• jd3_job_status_inputs_were_bad : protocols::jd3
• jd3_job_status_success : protocols::jd3
• JGJobNodeAP : protocols::jd3
• JGJobNodeCAP : protocols::jd3
• JGJobNodeCOP : protocols::jd3
• JGJobNodeOP : protocols::jd3
• JGResultNodeAP : protocols::jd3
• JGResultNodeCAP : protocols::jd3
• JGResultNodeCOP : protocols::jd3
• JGResultNodeOP : protocols::jd3
• JOB_COMPLETION : protocols::jd2::archive
• JOB_FAILED_NO_RETRY : protocols::jd2
• JOB_SUCCESS : protocols::jd2
• JobCOP : protocols::jd2 , protocols::jd3
• JobDAGNodeID : protocols::jd3
• JobDataFeaturesCOP : protocols::features
• JobDataFeaturesOP : protocols::features
• JobDigraphCOP : protocols::jd3
• JobDigraphOP : protocols::jd3
• JobDistributorCOP : protocols::jd3
• JobDistributorOP : protocols::jd3
• JobDistributorTracer() : protocols::jobdist
• JobExtractorCOP : protocols::jd3::job_distributors
• JobExtractorOP : protocols::jd3::job_distributors
• JobGenealogistCOP : protocols::jd3
• JobGenealogistOP : protocols::jd3
• JobInputterAP : protocols::jd2
• JobInputterCAP : protocols::jd2
• JobInputterCOP : protocols::jd2
• JobInputterCreatorCOP : protocols::jd2
• JobInputterCreatorOP : protocols::jd2
• JobInputterFactoryCOP : protocols::jd2
• JobInputterFactoryOP : protocols::jd2
• JobInputterOP : protocols::jd2
• jobname_dirhash() : protocols::canonical_sampling
• JobOP : protocols::jd2 , protocols::jd3
• JobOutputterCOP : protocols::jd2
• JobOutputterCreatorCOP : protocols::jd2
• JobOutputterCreatorOP : protocols::jd2
• JobOutputterFactoryCOP : protocols::jd2
• JobOutputterFactoryOP : protocols::jd2
• JobOutputterObserverAP : protocols::jd2
• JobOutputterObserverOP : protocols::jd2
• JobOutputterOP : protocols::jd2
• JobQueenCOP : protocols::jd3
• JobQueenOP : protocols::jd3
• JobResultCOP : protocols::jd3
• JobResultID : protocols::jd3
• JobResultOP : protocols::jd3
• JobRunnerCOP : protocols::jd3::job_distributors
• JobRunnerOP : protocols::jd3::job_distributors
• Jobs : protocols::jd2
• jobs_tracer() : protocols::jobdist
• JobsContainerCOP : protocols::jd2
• JobsContainerOP : protocols::jd2
• JobStatus : protocols::jd3
• JobSummaryCOP : protocols::jd3
• JobSummaryOP : protocols::jd3
• JobTrackerCOP : protocols::jd3
• JobTrackerOP : protocols::jd3
• JointScoreCOP : protocols::sic_dock
• JointScoreOP : protocols::sic_dock
• JointSequenceOperationOP : protocols::task_operations
• JRNL : core::io::pdb
• JSON_RPCCOP : protocols::rpc
• JSON_RPCOP : protocols::rpc
• judge_facing() : protocols::features::strand_assembly
• JUMP : core::id , core::pose::full_model_info , protocols::toolbox
• jump_distance() : core::kinematics
• JUMP_DOCK : protocols::stepwise::monte_carlo::mover
• jump_dofs() : protocols::environment
• jump_num_sym_dof() : core::pose::symmetry
• JUMP_TO_NEXT_IN_CHAIN : protocols::stepwise::monte_carlo::mover
• JUMP_TO_PREV_IN_CHAIN : protocols::stepwise::monte_carlo::mover
• jump_which_partitions() : core::kinematics
• JumpAtomAP : core::kinematics::tree
• JumpAtomCAP : core::kinematics::tree
• JumpAtomCOP : core::kinematics::tree
• JumpAtomOP : core::kinematics::tree
• JumpClaimAP : protocols::environment::claims , protocols::topology_broker::claims
• JumpClaimCAP : protocols::environment::claims , protocols::topology_broker::claims
• JumpClaimCOP : protocols::environment::claims , protocols::topology_broker::claims
• JumpClaimOP : protocols::environment::claims , protocols::topology_broker::claims
• JumpClaims : protocols::environment::claims , protocols::topology_broker::claims
• JumpDownstreamSelectorCOP : core::select::residue_selector
• JumpDownstreamSelectorOP : core::select::residue_selector
• JumpElements : protocols::environment::claims
• jumpfunc() : protocols::protein_interface_design::movers
• JumpIndexSelectorCOP : core::select::jump_selector
• JumpIndexSelectorOP : core::select::jump_selector
• JumpInfo : protocols::denovo_design::movers
• JumpingFoldConstraintsWrapperCOP : protocols::abinitio
• JumpingFoldConstraintsWrapperOP : protocols::abinitio
• JumpingFrameCOP : core::fragment
• JumpingFrameOP : core::fragment
• JumpList : protocols::jumping
• JumpMetricCOP : protocols::multistage_rosetta_scripts::cluster::metrics
• JumpMetricOP : protocols::multistage_rosetta_scripts::cluster::metrics
• JumpOutMoverCOP : protocols::moves
• JumpOutMoverOP : protocols::moves
• JumpRotamerSidechainMoverCOP : protocols::simple_moves::sidechain_moves
• JumpRotamerSidechainMoverOP : protocols::simple_moves::sidechain_moves
• Jumps : core::pose
• jumps_and_cuts_from_pose() : protocols::forge::methods
• jumps_connected_to_position() : protocols::forge::methods
• jumps_from_pose() : core::pose
• JumpSampleDataCOP : protocols::abinitio::abscript
• JumpSampleDataOP : protocols::abinitio::abscript
• JumpSelectorAP : core::select::jump_selector
• JumpSelectorCAP : core::select::jump_selector
• JumpSelectorCOP : core::select::jump_selector , protocols::jumping
• JumpSelectorCreatorCOP : core::select::jump_selector
• JumpSelectorCreatorOP : core::select::jump_selector
• JumpSelectorOP : core::select::jump_selector , protocols::jumping
• JumpSetupCOP : protocols::jumping
• JumpSetupOP : protocols::jumping
• jumpsfunc() : protocols::protein_interface_design::movers
• JumpStepWiseSamplerCOP : protocols::stepwise::sampler::jump
• JumpStepWiseSamplerOP : protocols::stepwise::sampler::jump
• JumpSubset : core::select::jump_selector
• JumpSubsetAP : core::select::jump_selector
• JumpSubsetCAP : core::select::jump_selector
• JumpSubsetCOP : core::select::jump_selector
• JumpSubsetOP : core::select::jump_selector
• JumpUpstreamSelectorCOP : core::select::residue_selector
• JumpUpstreamSelectorOP : core::select::residue_selector
• just_modeling_RNA() : core::import_pose , core::pose
• just_protein() : protocols::stepwise::modeler::protein
• just_rna() : protocols::stepwise::modeler::rna