Index – J

j() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) j_next() (pyrosetta.rosetta.core.pose.rna.BasePairStep method) Jcomputed() (pyrosetta.rosetta.core.scoring.RDC method) JCoupling (class in pyrosetta.rosetta.protocols.frag_picker.scores) jd2_used() (in module pyrosetta.rosetta.protocols.jd2) jd_output_suffix() (pyrosetta.rosetta.protocols.jd3.output.OutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputSpecification method) Jdipolar() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) Job (class in pyrosetta.rosetta.protocols.jd2) (class in pyrosetta.rosetta.protocols.jd3) job_available_on_command_line() (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter method) job_def_complex_type_name() (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) job_definition_xsd() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen 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) job_has_already_completed() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) job_has_completed() (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.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter 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.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) job_inputter_input_source() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor 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) job_inputter_input_source_to_string() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) job_outputter() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor 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) job_results_that_should_be_discarded() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen 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) job_tag() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) (pyrosetta.rosetta.protocols.jd3.LarvalJob method) job_tag_with_index_suffix() (pyrosetta.rosetta.protocols.jd3.LarvalJob method) JobDataFeaturesCreator (class in pyrosetta.rosetta.protocols.features) jobdef_tag() (pyrosetta.rosetta.protocols.jd3.InnerLarvalJob method) jobindex_on_originating_node() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) JobInputter (class in pyrosetta.rosetta.protocols.jd2) JobInputterCreator (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) JobQueen (class in pyrosetta.rosetta.protocols.jd3) JobResult (class in pyrosetta.rosetta.protocols.jd3) jobs_that_should_be_output() (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) JobsContainer (class in pyrosetta.rosetta.protocols.jd2) JobStatus (class in pyrosetta.rosetta.protocols.jd3) JobSummary (class in pyrosetta.rosetta.protocols.jd3) join() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) JointScore (class in pyrosetta.rosetta.protocols.sic_dock) JScoreEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) JsonEmitter (class in pyrosetta.rosetta.basic)

judge_facing() (in module pyrosetta.rosetta.protocols.features.strand_assembly) Jump (class in pyrosetta.rosetta.core.kinematics) 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.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.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) jump_atom_id() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) jump_backward() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) jump_distance() (in module pyrosetta.rosetta.core.kinematics) jump_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_exists() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_forward() (pyrosetta.rosetta.core.import_pose.libraries.RNA_PairingTemplate method) jump_id() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) jump_id_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) jump_id_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) jump_nr() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_num() (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) jump_num_sym_dof() (in module pyrosetta.rosetta.core.pose.symmetry) jump_pairs() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) jump_point() (pyrosetta.rosetta.core.kinematics.FoldTree method) jump_res_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) jump_selector_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader method) jump_which_partitions() (in module pyrosetta.rosetta.core.kinematics) JumpAtom (class in pyrosetta.rosetta.core.kinematics.tree) jumpAtoms() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) jumpAtoms_defined() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) JumpDownstreamSelector (class in pyrosetta.rosetta.core.select.residue_selector) JumpID (class in pyrosetta.rosetta.core.id) JumpIndexSelector (class in pyrosetta.rosetta.core.select.jump_selector) JumpingFrame (class in pyrosetta.rosetta.core.fragment) JumpNrEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) JumpRotamerSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) 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) JumpSelector (class in pyrosetta.rosetta.protocols.jumping) JumpSelectorLoader (class in pyrosetta.rosetta.protocols.parser) JumpSetup (class in pyrosetta.rosetta.protocols.jumping) JumpsFromAllPairings (class in pyrosetta.rosetta.protocols.jumping) JumpUpstreamSelector (class in pyrosetta.rosetta.core.select.residue_selector) 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_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.MembraneAbinitio method)