Index – J

j() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) (pyrosetta.rosetta.protocols.frag_picker.Contact method) j_next() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) JacobianStructure (class in pyrosetta.rosetta.core.kinematics.jacobian) JacobiLoopClosureMover (class in pyrosetta.rosetta.protocols.loops.loop_closure.jacobi) JacobiLoopClosureMoverCreator (class in pyrosetta.rosetta.protocols.loops.loop_closure.jacobi) jagged_array_double_std_allocator_double_t (class in pyrosetta.rosetta.protocols.mean_field) jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t (class in pyrosetta.rosetta.protocols.mean_field) jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t (class in pyrosetta.rosetta.protocols.mean_field) Jcomputed() (pyrosetta.rosetta.core.scoring.RDC method) JCoupling (class in pyrosetta.rosetta.protocols.frag_picker.scores) JCouplingIO (class in pyrosetta.rosetta.protocols.frag_picker) JD2 (pyrosetta.rosetta.basic.ProfTag attribute) JD2_INIT_MOVER (pyrosetta.rosetta.basic.ProfTag attribute) JD2_OUTPUT (pyrosetta.rosetta.basic.ProfTag attribute) JD2_SILENT_OUTPUTTER (pyrosetta.rosetta.basic.ProfTag attribute) jd2_used() (in module pyrosetta.rosetta.protocols.jd2) JD2Failure (class in pyrosetta.rosetta.protocols.jd2) jd3_job_previously_executed (pyrosetta.rosetta.protocols.jd3.JobStatus attribute) jd3_job_status_failed_do_not_retry (pyrosetta.rosetta.protocols.jd3.JobStatus attribute) jd3_job_status_failed_max_retries (pyrosetta.rosetta.protocols.jd3.JobStatus attribute) jd3_job_status_failed_retry (pyrosetta.rosetta.protocols.jd3.JobStatus attribute) jd3_job_status_failed_w_exception (pyrosetta.rosetta.protocols.jd3.JobStatus attribute) jd3_job_status_inputs_were_bad (pyrosetta.rosetta.protocols.jd3.JobStatus attribute) jd3_job_status_success (pyrosetta.rosetta.protocols.jd3.JobStatus attribute) jd_output_suffix() (pyrosetta.rosetta.protocols.jd3.output.MultipleOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) Jdipolar() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) Jdipolar_computed_ (pyrosetta.rosetta.core.scoring.RDC property) JGJobNode (class in pyrosetta.rosetta.protocols.jd3) JGResultNode (class in pyrosetta.rosetta.protocols.jd3) JJH_Minimizer (class in pyrosetta.rosetta.core.optimization) Job (class in pyrosetta.rosetta.protocols.jd2) (class in pyrosetta.rosetta.protocols.jd3) job_available_on_command_line() (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputter method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter method) job_complete (pyrosetta.toolbox.py_jobdistributor.PyJobDistributor property) job_dag() (pyrosetta.rosetta.protocols.jd3.JobDigraphUpdater method) job_dag_node() (pyrosetta.rosetta.protocols.jd3.JGJobNode method) job_def_complex_type_name() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen static method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen static method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen static method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen static method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker static method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen static method) job_definition_xsd() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) job_failed() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) JOB_FAILURE_TAG (pyrosetta.rosetta.basic.mpi.mpi_tags attribute) JOB_GO_TAG (pyrosetta.rosetta.basic.mpi.mpi_tags attribute) job_has_already_completed() (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter method) job_has_completed() (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) job_id() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) job_index() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) job_inputter() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) job_inputter_input_source() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) job_inputter_input_source_to_string() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter static method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter static method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter static method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter static method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter static method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputter static method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter static method) (pyrosetta.rosetta.protocols.jd2.JobInputter static method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter static method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter static method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter static method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter static method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputter static method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter static method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter static method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter static method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter static method) job_node() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) job_offset() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) job_options (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryPreliminaryLarvalJob property) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob property) (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJob property) job_outputter() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.JobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.jd2.ShuffleFileSystemJobDistributor method) (pyrosetta.rosetta.protocols.jd2.VectorPoseJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) job_queue_empty() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) job_result_id() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.ResultElements method) job_results (pyrosetta.rosetta.protocols.jd3.CompletedJobOutput property) job_results_that_should_be_discarded() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) job_succeeded() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor method) JOB_SUCCESS_TAG (pyrosetta.rosetta.basic.mpi.mpi_tags attribute) job_tag (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryPreliminaryLarvalJob property) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob property) (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJob property) job_tag() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) job_tag_with_index_suffix() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) JobDataFeatures (class in pyrosetta.rosetta.protocols.features) JobDataFeaturesCreator (class in pyrosetta.rosetta.protocols.features) jobdef_tag() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelInnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) JobDigraph (class in pyrosetta.rosetta.protocols.jd3) JobDigraphUpdater (class in pyrosetta.rosetta.protocols.jd3) JobDirectedEdge (class in pyrosetta.rosetta.protocols.jd3) JobDirectedNode (class in pyrosetta.rosetta.protocols.jd3) JOBDIST_OUTPUT_TAG (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) JobDistributor (class in pyrosetta.rosetta.protocols.jd2) (class in pyrosetta.rosetta.protocols.jd3) JobDistributorFactory (class in pyrosetta.rosetta.protocols.jd2) (class in pyrosetta.rosetta.protocols.jd3) JobExtractor (class in pyrosetta.rosetta.protocols.jd3.job_distributors) JobGenealogist (class in pyrosetta.rosetta.protocols.jd3) jobindex_on_originating_node() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_ResultsSummaryBase method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_RMSDToBestSummary method) (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) JobInputter (class in pyrosetta.rosetta.protocols.jd2) JobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) JobInputterFactory (class in pyrosetta.rosetta.protocols.jd2) JobOutputIndex (class in pyrosetta.rosetta.protocols.jd3) JobOutputter (class in pyrosetta.rosetta.protocols.jd2) JobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) JobOutputterFactory (class in pyrosetta.rosetta.protocols.jd2) JobOutputterObserver (class in pyrosetta.rosetta.protocols.jd2) JobQueen (class in pyrosetta.rosetta.protocols.jd3) JobResult (class in pyrosetta.rosetta.protocols.jd3) JobResultID_hash (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) jobs_are_still_running() (pyrosetta.rosetta.protocols.jd3.dag_node_managers.EvenlyPartitionedNodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.NodeManager method) (pyrosetta.rosetta.protocols.jd3.dag_node_managers.SimpleNodeManager method) jobs_remain() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) jobs_that_should_be_output() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) JobsContainer (class in pyrosetta.rosetta.protocols.jd2) JobStatus (class in pyrosetta.rosetta.protocols.jd3) JobSummary (class in pyrosetta.rosetta.protocols.jd3) JobTracker (class in pyrosetta.rosetta.protocols.jd3) join() (in module pyrosetta.rosetta.utility) join_two_poses_by_jump() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) JointScore (class in pyrosetta.rosetta.protocols.sic_dock) JointSequenceOperation (class in pyrosetta.rosetta.protocols.task_operations) JointSequenceOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) journal_title() (pyrosetta.rosetta.basic.citation_manager.Citation method) JQKey (class in pyrosetta.rosetta.protocols.jd3) JRNL (pyrosetta.rosetta.core.io.pdb.RecordType attribute) JScoreEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) JScoreEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) Json_based_CDR_Detector (class in pyrosetta.rosetta.protocols.antibody.grafting) JSON_RPC (class in pyrosetta.rosetta.protocols.rpc) JsonEmitter (class in pyrosetta.rosetta.basic) JSONFormattedLoopsFileReader (class in pyrosetta.rosetta.protocols.loops) JSONStructureStoreBackend (class in pyrosetta.rosetta.protocols.indexed_structure_store)

judge_facing() (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) judge_sw_dis_too_close() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) judge_sw_inter_dis() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) judge_sw_torsion() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) Jump (class in pyrosetta.rosetta.core.kinematics) JUMP (pyrosetta.rosetta.core.id.TorsionType attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) jump (pyrosetta.rosetta.protocols.denovo_design.movers.CutAndJump property) (pyrosetta.rosetta.protocols.ligand_docking.Ligand_info property) JUMP (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) jump() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) jump_ (pyrosetta.rosetta.protocols.jumping.JumpSelector.JumpWeightDef property) (pyrosetta.rosetta.protocols.jumping.JumpSetup.JumpDef property) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup.JumpDef property) jump_atom() (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) jump_atom1() (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) jump_atom2() (pyrosetta.rosetta.protocols.topology_broker.claims.JumpClaim method) jump_atom_id() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) jump_atoms() (pyrosetta.rosetta.protocols.jumping.JumpSample method) jump_backward() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) jump_change_frequency() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) jump_clones() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) jump_dbase_fname() (pyrosetta.rosetta.protocols.splice.RBOutMover method) jump_direction() (pyrosetta.rosetta.core.conformation.symmetry.SymDof method) jump_distance() (in module pyrosetta.rosetta.core.kinematics) JUMP_DOCK (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AttachmentType attribute) jump_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_exists() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_follows() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) jump_forward() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) jump_from_foldtree() (pyrosetta.rosetta.protocols.splice.RBOutMover method) jump_from_internal_coords() (in module pyrosetta.rosetta.core.kinematics.inverse) jump_histogram() (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) jump_histogram_binwidth() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) jump_histogram_binwidth_rotvector() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) jump_histogram_boxsize() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) jump_id() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate_info method) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) jump_ids() (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info method) jump_is_independent() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) jump_library() (pyrosetta.rosetta.protocols.splice.RBInMover method) jump_library_file() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) jump_mover() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) jump_nr() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_num() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) jump_num_substrate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) jump_num_sym_dof() (in module pyrosetta.rosetta.core.pose.symmetry) jump_number() (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) jump_pairs() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) Jump_point (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) jump_point() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_res_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) jump_sample() (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleData method) jump_selector_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader static method) jump_selector_xml_schema_group_name() (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory static method) jump_set() (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) JUMP_TO_NEXT_IN_CHAIN (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AttachmentType attribute) JUMP_TO_PREV_IN_CHAIN (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AttachmentType attribute) jump_which_partitions() (in module pyrosetta.rosetta.core.kinematics) JumpAtom (class in pyrosetta.rosetta.core.kinematics.tree) jumpAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) jumpAtoms_defined() (pyrosetta.rosetta.protocols.jumping.ResiduePairJump method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) JumpClaim (class in pyrosetta.rosetta.protocols.environment.claims) (class in pyrosetta.rosetta.protocols.topology_broker.claims) JumpClaim.ClaimRight (class in pyrosetta.rosetta.protocols.topology_broker.claims) JumpDownstreamSelector (class in pyrosetta.rosetta.core.select.residue_selector) JumpDownstreamSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) JumpElement (class in pyrosetta.rosetta.protocols.environment.claims) JumpEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) JumpForResidue (class in pyrosetta.rosetta.core.select.jump_selector) JumpForResidueCreator (class in pyrosetta.rosetta.core.select.jump_selector) JumpID (class in pyrosetta.rosetta.core.id) jumpid_ (pyrosetta.rosetta.protocols.loop_grower.SheetPositions property) JumpIndexSelector (class in pyrosetta.rosetta.core.select.jump_selector) JumpIndexSelectorCreator (class in pyrosetta.rosetta.core.select.jump_selector) JumpingFoldConstraintsWrapper (class in pyrosetta.rosetta.protocols.abinitio) JumpingFoldConstraintsWrapper.StageID (class in pyrosetta.rosetta.protocols.abinitio) JumpingFrame (class in pyrosetta.rosetta.core.fragment) JumpMetric (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics) JumpMetric.DOF (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics) JumpMetricCreator (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics) JumpNrEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) JumpNrEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) JumpOutMover (class in pyrosetta.rosetta.protocols.moves) JumpRotamerSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) JumpRotamerSidechainMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) jumps() (pyrosetta.rosetta.protocols.jumping.JumpSample method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) jumps_and_cuts_from_pose() (in module pyrosetta.rosetta.protocols.forge.methods) jumps_connected_to_position() (in module pyrosetta.rosetta.protocols.forge.methods) jumps_from_pose() (in module pyrosetta.rosetta.core.pose) jumps_info() (pyrosetta.rosetta.core.pose.copydofs.CopyDofsInfo method) JumpSample (class in pyrosetta.rosetta.protocols.jumping) JumpSampleData (class in pyrosetta.rosetta.protocols.abinitio.abscript) JumpSampleDataCreator (class in pyrosetta.rosetta.protocols.abinitio.abscript) JumpSelector (class in pyrosetta.rosetta.core.select.jump_selector) (class in pyrosetta.rosetta.protocols.jumping) JumpSelector.JumpWeightDef (class in pyrosetta.rosetta.protocols.jumping) JumpSelectorCreator (class in pyrosetta.rosetta.core.select.jump_selector) JumpSelectorFactory (class in pyrosetta.rosetta.core.select.jump_selector) JumpSelectorLoader (class in pyrosetta.rosetta.protocols.parser) JumpSelectorLoaderCreator (class in pyrosetta.rosetta.protocols.parser) JumpSetup (class in pyrosetta.rosetta.protocols.jumping) JumpSetup.JumpDef (class in pyrosetta.rosetta.protocols.jumping) JumpsFromAllPairings (class in pyrosetta.rosetta.protocols.jumping) JumpStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.jump) JumpUpstreamSelector (class in pyrosetta.rosetta.core.select.residue_selector) JumpUpstreamSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) just_min_after_mutation_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) just_modeling_RNA() (in module pyrosetta.rosetta.core.import_pose) (in module pyrosetta.rosetta.core.pose) just_protein() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) just_rna() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) just_simple_cycles() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) just_smooth_cycles() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method)