Index – J

j() (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.BasePairStep method) j_next() (pyrosetta.rosetta.protocols.rna.denovo.base_pairs.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) JD2ResourceManager (class in pyrosetta.rosetta.protocols.jd2) JD2ResourceManagerCreator (class in pyrosetta.rosetta.protocols.jd2) JD2ResourceManagerJobInputter (class in pyrosetta.rosetta.protocols.jd2) JD2ResourceManagerJobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) Jdipolar() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) Job (class in pyrosetta.rosetta.protocols.jd2) 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_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_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.JD2ResourceManagerJobInputter 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_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) JobDataFeaturesCreator (class in pyrosetta.rosetta.protocols.features) 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) JobOptions (class in pyrosetta.rosetta.basic.resource_manager) JobOutputter (class in pyrosetta.rosetta.protocols.jd2) JobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) JobsContainer (class in pyrosetta.rosetta.protocols.jd2) 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.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.rna.denovo.libraries.RNA_PairingTemplate method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.toolbox.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.protocols.rna.denovo.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.protocols.rna.denovo.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)