Index – M

M (pyrosetta.rosetta.core.kinematics.Stub property) m1_b1_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_b1_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_b2_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_b2_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_m2_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m1_m2_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m2_b1_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m2_b1_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m2_b2_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) m2_b2_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) maca (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) Magenta (pyrosetta.rosetta.utility.CSI.CSI_Enum attribute) magentic_anisotropy_q_coeff() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) magentic_anisotropy_r_coeff() (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) magnetic_anisotropy_effect() (in module pyrosetta.rosetta.core.scoring.rna.chemical_shift) magnitude() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) magnitude_error() (pyrosetta.rosetta.numeric.Quaternion_double_t method) magnitude_rotation() (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) magnitude_squared() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.Quaternion_double_t method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) magnitude_squared_error() (pyrosetta.rosetta.numeric.Quaternion_double_t method) magnitude_translation() (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) main() (in module pyrosetta.network.rosetta_udp_to_tcp_bridge) main_atom() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) main_chain_torsion_set() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) main_chain_torsion_set_lists() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) main_chain_torsion_set_lists_real() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) main_chain_torsion_set_save() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) main_chain_torsion_sets() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) main_plain_mover() (in module pyrosetta.rosetta.protocols.jobdist) main_plain_pdb_mover() (in module pyrosetta.rosetta.protocols.jobdist) mainchain_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) mainchain_atoms() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) mainchain_dihedral_values() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) mainchain_glycosidic_bond_acceptor() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) mainchain_path() (in module pyrosetta.rosetta.core.chemical) mainchain_potentials_match() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) mainchain_torsion() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) mainchain_torsions() (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) mainchain_torsions_covered() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) MainchainScoreTable (class in pyrosetta.rosetta.core.chemical.mainchain_potential) MainchainTorsionReporter (class in pyrosetta.rosetta.core.pack.dunbrack) MainChainTorsionSet (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein) MainchainTorsionType (class in pyrosetta.rosetta.core.id) maintain_links() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) major_radius() (pyrosetta.rosetta.numeric.linear_algebra.EllipseParameters method) make() (pyrosetta.rosetta.core.chemical.ResidueType static method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeABEGO_SS_Score method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAmbigCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeAtomPairConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeBFactor method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDihedralConstraintsScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeDisulfideIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentAllAtomCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentChunkCrms method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentCrmsdResDepth method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentDME method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeFragmentScoringMethod method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeGunnCostScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicityProfileSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeHydrophobicitySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeInterbondAngleScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeJCoupling method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeLAMBEGO_Similarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPhiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeMidPsiOut method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiRmsd method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePhiPsiSquareWell method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreBlosum62 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreDistWeight method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreStructL1 method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProfileScoreSubMatrix method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeScoreEValuator method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondaryIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSecondarySimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSequenceIdentity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeSolventAccessibility method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTalosSSSimilarity method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeTorsionBinSimilarity method) make_aligned_residue() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer method) make_asymmetric_movemap() (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer static method) make_asymmetric_pose() (in module pyrosetta.rosetta.core.pose.symmetry) make_atom_map() (in module pyrosetta.rosetta.core.pose) make_atr_rep_grid() (in module pyrosetta.rosetta.protocols.ligand_docking) make_atr_rep_grid_without_ligand() (in module pyrosetta.rosetta.protocols.ligand_docking) make_atr_rep_grid_without_ligands() (in module pyrosetta.rosetta.protocols.ligand_docking) make_base_pair_aware_fold_tree() (in module pyrosetta.rosetta.protocols.dna) MAKE_BASE_PAIR_MOVE (pyrosetta.rosetta.basic.ProfTag attribute) make_base_pair_mutation() (in module pyrosetta.rosetta.protocols.motifs) MAKE_BASE_STEP_MOVE (pyrosetta.rosetta.basic.ProfTag attribute) make_centroid() (in module pyrosetta.rosetta.core.chemical) make_chain() (in module pyrosetta.rosetta.core.io.mmtf) make_chi_move() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) make_claim() (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim static method) (pyrosetta.rosetta.protocols.environment.claims.EnvClaim static method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim static method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim static method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim static method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim static method) make_coarse_pose() (in module pyrosetta.rosetta.core.import_pose) make_compatible_with_ROCS_custom_ForceField() (pyrosetta.rosetta.protocols.pockets.GenPharmacophore method) make_compound_statement() (in module pyrosetta.rosetta.basic.database) make_conditional_index() (in module pyrosetta.rosetta.core.pack.dunbrack) make_continuous_true_regions_in_bool_vector() (in module pyrosetta.rosetta.protocols.enzdes.enzutil) make_cut_at_moving_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) make_Cx() (in module pyrosetta.rosetta.protocols.sic_dock) make_disulfide() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) make_disulfide_fast() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) make_disulfides() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) make_dna_mutations() (in module pyrosetta.rosetta.protocols.motifs) make_dna_rigid() (in module pyrosetta.rosetta.protocols.relax) make_extended_coarse_pose() (in module pyrosetta.rosetta.core.import_pose) make_fibril() (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) make_hbBasetoAcc_unitvector() (in module pyrosetta.rosetta.core.scoring.hbonds) make_hotspot_foldtree() (in module pyrosetta.rosetta.protocols.protein_interface_design) make_index() (in module pyrosetta.rosetta.core.pack.dunbrack) make_index_selector() (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) make_initial_power_diagram() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) make_interface_combos() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) make_jump() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) make_ligand_only_pose() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) make_local_bb_change() (pyrosetta.rosetta.protocols.loophash.LocalInserter method) (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) make_local_bb_change_close_gaps() (pyrosetta.rosetta.protocols.loophash.LocalInserter method) (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) make_local_bb_change_include_cut() (pyrosetta.rosetta.protocols.loophash.LocalInserter method) (pyrosetta.rosetta.protocols.loophash.LocalInserter_SimpleMin method) make_move() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) make_movie() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) make_multi_pose_grids() (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) make_multifunc() (pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap method) (pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap method) make_new_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet method) make_new_pose() (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) make_new_sphere() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) make_new_symmetric_PackerTask_by_requested_method() (in module pyrosetta.rosetta.core.pack) make_no_pore_parameters() (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) make_partially_soft_etable() (pyrosetta.rosetta.core.scoring.ScoringManager method) make_phosphate_nomenclature_matches_mini() (in module pyrosetta.rosetta.core.pose.rna) make_points() (in module pyrosetta.rosetta.numeric.kdtree) make_pose_from_design() (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) make_pose_from_frags() (in module pyrosetta.rosetta.core.fragment) make_pose_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) make_pose_from_sequence() (in module pyrosetta.rosetta.core.pose) make_pre_proline_potential() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) make_pymol_script() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) make_rasmol_format_file() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) make_residue_mask_symmetric() (in module pyrosetta.rosetta.core.pose.symmetry) make_rid_posenum() (in module pyrosetta.rosetta.core.pose) MAKE_ROT_LIB (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) make_sec() (pyrosetta.rosetta.protocols.hybridization.TMalign method) make_segtag_with_dashes() (in module pyrosetta.rosetta.utility) make_semisymmetric_movemap() (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer static method) make_sequence_shift() (pyrosetta.rosetta.protocols.loops.Loops method) make_simple_fold_tree_from_jump_frame() (in module pyrosetta.rosetta.core.fragment) make_single_mutants() (in module pyrosetta.rosetta.protocols.dna) make_specific_mutant() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) make_spline() (in module pyrosetta.rosetta.numeric.interpolation) make_star_foldtree() (in module pyrosetta.rosetta.protocols.forge.methods) make_strand_info_str() (in module pyrosetta.rosetta.protocols.denovo_design.components) make_strand_neighbor_two() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) make_stub_scorefxn() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) make_subdirs() (in module pyrosetta.rosetta.protocols.dna) make_sure_full_model_info_is_setup() (in module pyrosetta.rosetta.core.pose.full_model_info) make_sure_vdw_cached_rep_screen_info_is_setup() (in module pyrosetta.rosetta.protocols.scoring) make_symmetric_fibril() (in module pyrosetta.rosetta.protocols.fibril) make_symmetric_movemap() (in module pyrosetta.rosetta.core.pose.symmetry) make_symmetric_PackerTask_by_truncation() (in module pyrosetta.rosetta.core.pack) make_symmetric_pdb_info() (in module pyrosetta.rosetta.core.pose.symmetry) make_symmetric_pose() (in module pyrosetta.rosetta.core.pose.symmetry) make_symmetric_task() (in module pyrosetta.rosetta.core.pack) make_table() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) make_tag() (in module pyrosetta.rosetta.utility) make_tag_with_dashes() (in module pyrosetta.rosetta.utility) make_three_fold_symmetry_90_210_330() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) make_two_fold_symmetry_0_180() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) make_two_fold_symmetry_135_315() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) make_variants_match() (in module pyrosetta.rosetta.protocols.stepwise.modeler) make_vector() (in module pyrosetta.rosetta.utility.tools) make_vector1() (in module pyrosetta.rosetta.utility.tools) MakeABEGO_SS_Score (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeAmbigCSScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeAsymmetricStructureDataMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) MakeAsymmetricStructureDataMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) MakeAtomPairConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeBFactor (class in pyrosetta.rosetta.protocols.frag_picker.scores) makebinary() (pyrosetta.rosetta.protocols.sic_dock.XfoxmScore method) MakeBundle (class in pyrosetta.rosetta.protocols.helical_bundle) MakeBundleCreator (class in pyrosetta.rosetta.protocols.helical_bundle) MakeBundleHelix (class in pyrosetta.rosetta.protocols.helical_bundle) MakeBundleHelixCreator (class in pyrosetta.rosetta.protocols.helical_bundle) MakeCanonicalHelix (class in pyrosetta.rosetta.protocols.membrane.benchmark) MakeCanonicalHelixCreator (class in pyrosetta.rosetta.protocols.membrane.benchmark) MakeConstScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeCSScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeDihedralConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeDisulfideDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeDisulfideIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentAllAtomCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentChunkCrms (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentCrmsdResDepth (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentDME (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeFragmentScoringMethod (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeGunnCostScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeHydrophobicityProfileSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeHydrophobicitySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeInterbondAngleScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeJCoupling (class in pyrosetta.rosetta.protocols.frag_picker.scores) makeJunctions_apply() (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) MakeJunctionsMover (class in pyrosetta.rosetta.protocols.pose_creation) MakeJunctionsMover.Design (class in pyrosetta.rosetta.protocols.pose_creation) MakeJunctionsMoverCreator (class in pyrosetta.rosetta.protocols.pose_creation) MakeLAMBEGO_Similarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeLatticeMover (class in pyrosetta.rosetta.protocols.cryst) MakeLatticeMoverCreator (class in pyrosetta.rosetta.protocols.cryst) MakeLayerMover (class in pyrosetta.rosetta.protocols.cryst) MakeLayerMoverCreator (class in pyrosetta.rosetta.protocols.cryst) MakeMidPhiOut (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeMidPsiOut (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePartialSecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePCS_FragDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePhi (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePhiPsiRmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePhiPsiSquareWell (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePolyXMover (class in pyrosetta.rosetta.protocols.pose_creation) MakePolyXMoverCreator (class in pyrosetta.rosetta.protocols.pose_creation) MakeProfileScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeProfileScoreBlosum62 (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeProfileScoreDistWeight (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeProfileScoreL1 (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeProfileScoreStructL1 (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeProfileScoreSubMatrix (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeProlinePhiScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakePsi (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeRamaScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeRDCScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeRotLibJob (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeRotLibJobInputter (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeRotLibJobInputterCreator (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeRotLibMover (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeRotLibOptionsData (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeRotLibPolymerType (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeScoreEValuator (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeSecondaryIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeSecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeSequenceIdentity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeSolventAccessibility (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeStarTopologyMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) MakeStarTopologyMoverCreator (class in pyrosetta.rosetta.protocols.rbsegment_relax) MakeTalosSSSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeTorsionBinSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeVector() (pyrosetta.rosetta.numeric.MathVector_double_t method) MALONYLATION (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) manager (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet property) manager() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) manipulate_cut_bias() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) manual_call() (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) manual_refine_pdb() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) manualPackerTaskGen() (pyrosetta.rosetta.protocols.forge.remodel.RemodelWorkingSet method) map() (pyrosetta.rosetta.basic.datacache.CacheableResRotPairFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringIntegerMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.basic.datacache.CacheableUint64MathMatrixFloatMap method) (pyrosetta.rosetta.basic.datacache.WriteableCacheableMap method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) map2keyvector() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) map2target() (pyrosetta.rosetta.protocols.abinitio.Template method) map2template() (pyrosetta.rosetta.protocols.abinitio.Template method) map_by_residue_subsets() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) map_char_double (class in pyrosetta.rosetta.std) map_char_protocols_pose_sewing_movers_SeedSettings (class in pyrosetta.rosetta.std) map_char_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_char_std_pair_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.std) map_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t_std_allocator_std_pair_const_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t (class in pyrosetta.rosetta.std) map_char_to_torsion_bin() (in module pyrosetta.rosetta.core.conformation) map_char_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_char_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.std) map_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_char_utility_vector1_std_string_std_allocator_std_string_t (class in pyrosetta.rosetta.std) map_constraints_from_original_pose() (in module pyrosetta.rosetta.core.scoring.constraints) map_core_chemical_AA_double (class in pyrosetta.rosetta.std) map_core_chemical_AA_std_pair_double_double_t_std_allocator_std_pair_const_core_chemical_AA_std_pair_double_double_t (class in pyrosetta.rosetta.std) map_core_chemical_AA_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.std) map_core_environment_LocalPosition_double (class in pyrosetta.rosetta.std) map_core_id_AtomID_bool (class in pyrosetta.rosetta.std) map_core_id_AtomID_core_id_AtomID (class in pyrosetta.rosetta.std) map_core_id_AtomID_double (class in pyrosetta.rosetta.std) map_core_id_AtomID_unsigned_long (class in pyrosetta.rosetta.std) map_core_id_AtomID_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_core_id_AtomID_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.std) map_core_scoring_rmsd_atoms_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_core_scoring_rmsd_atoms_utility_vector1_std_string_std_allocator_std_string_t (class in pyrosetta.rosetta.std) map_core_scoring_ScoreType_double (class in pyrosetta.rosetta.std) map_for_residue_exists() (pyrosetta.rosetta.protocols.chromophore.ChromophoreDataReader method) map_from_reference() (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) map_from_spectrum() (in module pyrosetta.rosetta.protocols.electron_density) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) map_index() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) map_int_int (class in pyrosetta.rosetta.std) map_int_protocols_legacy_sewing_Model (class in pyrosetta.rosetta.std) map_int_utility_vector0_float_std_allocator_float_t_std_allocator_std_pair_const_int_utility_vector0_float_std_allocator_float_t (class in pyrosetta.rosetta.std) map_of_weighted_scores() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) map_pairings2target() (pyrosetta.rosetta.protocols.abinitio.Template method) map_pairings2template() (pyrosetta.rosetta.protocols.abinitio.Template method) map_phores() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) map_protocols_antibody_CDRNameEnum_protocols_loops_Loop (class in pyrosetta.rosetta.std) map_protocols_antibody_CDRNameEnum_utility_vector1_core_chemical_AA_std_allocator_core_chemical_AA_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_core_chemical_AA_std_allocator_core_chemical_AA_t (class in pyrosetta.rosetta.std) map_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBPose_std_allocator_protocols_antibody_CDRDBPose_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBPose_std_allocator_protocols_antibody_CDRDBPose_t (class in pyrosetta.rosetta.std) map_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBSequence_std_allocator_protocols_antibody_CDRDBSequence_t_std_allocator_std_pair_const_protocols_antibody_CDRNameEnum_utility_vector1_protocols_antibody_CDRDBSequence_std_allocator_protocols_antibody_CDRDBSequence_t (class in pyrosetta.rosetta.std) map_protocols_antibody_clusters_CDRClusterEnum_utility_vector1_protocols_antibody_design_MutantPosition_std_allocator_protocols_antibody_design_MutantPosition_t_std_allocator_std_pair_const_protocols_antibody_clusters_CDRClusterEnum_utility_vector1_protocols_antibody_design_MutantPosition_std_allocator_protocols_antibody_design_MutantPosition_t (class in pyrosetta.rosetta.std) map_protocols_carbohydrates_GlycanSequon_std_string (class in pyrosetta.rosetta.std) map_residues() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) map_seq1_seq2() (in module pyrosetta.rosetta.core.sequence) map_std_pair_core_chemical_AA_core_chemical_AA_t_double_std_less_std_pair_core_chemical_AA_core_chemical_AA_t_std_allocator_std_pair_const_std_pair_core_chemical_AA_core_chemical_AA_double_t (class in pyrosetta.rosetta.std) map_std_pair_core_id_AtomID_core_id_AtomID_t_utility_vector1_double_std_allocator_double_t_std_less_std_pair_core_id_AtomID_core_id_AtomID_t_std_allocator_std_pair_const_std_pair_core_id_AtomID_core_id_AtomID_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.std) map_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_protocols_legacy_sewing_HashResult_std_less_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_t_std_allocator_std_pair_const_std_pair_protocols_legacy_sewing_Basis_protocols_legacy_sewing_Basis_protocols_legacy_sewing_HashResult_t (class in pyrosetta.rosetta.std) map_std_pair_std_string_std_string_t_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t_std_less_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_pair_std_string_std_string_utility_vector1_core_chemical_carbohydrates_LinkageConformerData_std_allocator_core_chemical_carbohydrates_LinkageConformerData_t (class in pyrosetta.rosetta.std) map_std_pair_unsigned_long_std_string_t_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t_std_less_std_pair_unsigned_long_std_string_t_std_allocator_std_pair_const_std_pair_unsigned_long_std_string_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t (class in pyrosetta.rosetta.std) map_std_pair_unsigned_long_unsigned_long_t_std_set_protocols_sewing_hashing_LigandCoordInfo_t_std_less_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_std_set_protocols_sewing_hashing_LigandCoordInfo_t (class in pyrosetta.rosetta.std) map_std_pair_unsigned_long_unsigned_long_t_unsigned_long_std_less_std_pair_unsigned_long_unsigned_long_t_std_allocator_std_pair_const_std_pair_unsigned_long_unsigned_long_unsigned_long_t (class in pyrosetta.rosetta.std) map_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_unsigned_long_std_less_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_t_std_allocator_std_pair_const_std_shared_ptr_const_protocols_toolbox_match_enzdes_util_InvrotTreeNodeBase_unsigned_long_t (class in pyrosetta.rosetta.std) map_std_string_bool (class in pyrosetta.rosetta.std) map_std_string_char (class in pyrosetta.rosetta.std) map_std_string_core_chemical_AA (class in pyrosetta.rosetta.std) map_std_string_core_chemical_carbohydrates_RootData (class in pyrosetta.rosetta.std) map_std_string_core_chemical_carbohydrates_SugarModificationsNomenclatureTableRow (class in pyrosetta.rosetta.std) map_std_string_core_conformation_symmetry_VirtualCoordinate (class in pyrosetta.rosetta.std) map_std_string_core_id_NamedAtomID (class in pyrosetta.rosetta.std) map_std_string_core_io_CisPeptideInformation (class in pyrosetta.rosetta.std) map_std_string_core_io_ModifiedResidueInformation (class in pyrosetta.rosetta.std) map_std_string_core_io_nmr_ParaIon (class in pyrosetta.rosetta.std) map_std_string_core_io_nmr_SpinlabelDatabaseEntry (class in pyrosetta.rosetta.std) map_std_string_core_io_pdb_RecordType (class in pyrosetta.rosetta.std) map_std_string_core_pose_Pose (class in pyrosetta.rosetta.std) map_std_string_core_scoring_rmsd_atoms (class in pyrosetta.rosetta.std) map_std_string_double (class in pyrosetta.rosetta.std) map_std_string_float (class in pyrosetta.rosetta.std) map_std_string_int (class in pyrosetta.rosetta.std) map_std_string_numeric_interpolation_spline_LinearFunction (class in pyrosetta.rosetta.std) map_std_string_numeric_xyzVector_double_t_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t (class in pyrosetta.rosetta.std) map_std_string_protocols_denovo_design_components_Alias (class in pyrosetta.rosetta.std) map_std_string_protocols_scoring_methods_pcs2_PcsInputFile (class in pyrosetta.rosetta.std) map_std_string_protocols_scoring_methods_pcs_PCS_file_data (class in pyrosetta.rosetta.std) map_std_string_protocols_scoring_methods_pcsTs1_PCS_file_data_Ts1 (class in pyrosetta.rosetta.std) map_std_string_protocols_scoring_methods_pcsTs2_PCS_file_data_Ts2 (class in pyrosetta.rosetta.std) map_std_string_protocols_scoring_methods_pcsTs3_PCS_file_data_Ts3 (class in pyrosetta.rosetta.std) map_std_string_protocols_scoring_methods_pcsTs4_PCS_file_data_Ts4 (class in pyrosetta.rosetta.std) map_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t_std_allocator_std_pair_const_std_string_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t (class in pyrosetta.rosetta.std) map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t (class in pyrosetta.rosetta.std) map_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t (class in pyrosetta.rosetta.std) map_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t (class in pyrosetta.rosetta.std) map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t (class in pyrosetta.rosetta.std) map_std_string_std_map_unsigned_long_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_double_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_double_t (class in pyrosetta.rosetta.std) map_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t (class in pyrosetta.rosetta.std) map_std_string_std_map_unsigned_long_std_string_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_string_t_std_allocator_std_pair_const_std_string_std_map_unsigned_long_std_string_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_string_t (class in pyrosetta.rosetta.std) map_std_string_std_pair_core_chemical_io_merge_residue_behavior_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_core_chemical_io_merge_residue_behavior_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t (class in pyrosetta.rosetta.std) map_std_string_std_pair_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t (class in pyrosetta.rosetta.std) map_std_string_std_pair_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_utility_vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_std_allocator_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t_std_allocator_std_pair_const_std_string_std_pair_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_utility_vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_std_allocator_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t (class in pyrosetta.rosetta.std) map_std_string_std_set_std_shared_ptr_basic_datacache_WriteableCacheableData_t_std_allocator_std_pair_const_std_string_std_set_std_shared_ptr_basic_datacache_WriteableCacheableData_t (class in pyrosetta.rosetta.std) map_std_string_std_set_std_string_t_std_allocator_std_pair_const_std_string_std_set_std_string_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_basic_MetricValueBase_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_MetricValueBase_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_basic_resource_manager_ResourceLoaderCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_resource_manager_ResourceLoaderCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_basic_resource_manager_ResourceLocatorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_basic_resource_manager_ResourceLocatorCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_const_core_chemical_Metapatch_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_core_chemical_Metapatch_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_protocols_pack_daemon_VectorExpression_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_const_utility_tag_Tag_t_std_allocator_std_pair_const_std_string_std_shared_ptr_const_utility_tag_Tag_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_pack_palette_PackerPaletteCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_palette_PackerPaletteCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_operation_ResLvlTaskOperationCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_pack_task_operation_TaskOperationCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_operation_TaskOperationCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_pack_task_ResfileCommand_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pack_task_ResfileCommand_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_pose_Pose_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pose_Pose_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_scoring_motif_MotifHash_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_scoring_motif_MotifHash_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_select_jump_selector_JumpSelectorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_jump_selector_JumpSelectorCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelector_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_select_residue_selector_ResidueSelectorCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_simple_metrics_SimpleMetricCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_numeric_expression_parser_VariableExpression_t_std_allocator_std_pair_const_std_string_std_shared_ptr_numeric_expression_parser_VariableExpression_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_protocols_filters_FilterCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_filters_FilterCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_protocols_moves_MoverCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_moves_MoverCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_multistage_rosetta_scripts_cluster_ClusterMetricCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_protocols_parser_DataLoaderCreator_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_parser_DataLoaderCreator_t (class in pyrosetta.rosetta.std) map_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t_std_allocator_std_pair_const_std_string_std_shared_ptr_protocols_splice_SpliceSegment_t (class in pyrosetta.rosetta.std) map_std_string_std_string (class in pyrosetta.rosetta.std) map_std_string_std_tuple_std_string_std_string_char_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_std_tuple_std_string_std_string_char_utility_vector1_std_string_std_allocator_std_string_t (class in pyrosetta.rosetta.std) map_std_string_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_double_t (class in pyrosetta.rosetta.std) map_std_string_std_vector_std_string_t_std_allocator_std_pair_const_std_string_std_vector_std_string_t (class in pyrosetta.rosetta.std) map_std_string_std_vector_std_vector_double_t_std_allocator_std_pair_const_std_string_std_vector_std_vector_double_t (class in pyrosetta.rosetta.std) map_std_string_std_vector_unsigned_long_t_std_allocator_std_pair_const_std_string_std_vector_unsigned_long_t (class in pyrosetta.rosetta.std) map_std_string_unsigned_long (class in pyrosetta.rosetta.std) map_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t_std_allocator_std_pair_const_std_string_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t (class in pyrosetta.rosetta.std) map_std_string_utility_vector1_char_std_allocator_char_t_std_allocator_std_pair_const_std_string_utility_vector1_char_std_allocator_char_t (class in pyrosetta.rosetta.std) map_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t_std_allocator_std_pair_const_std_string_utility_vector1_core_io_LinkInformation_std_allocator_core_io_LinkInformation_t (class in pyrosetta.rosetta.std) map_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t_std_allocator_std_pair_const_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t (class in pyrosetta.rosetta.std) map_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_const_core_chemical_Patch_std_allocator_std_shared_ptr_const_core_chemical_Patch_t (class in pyrosetta.rosetta.std) map_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_std_string_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t (class in pyrosetta.rosetta.std) map_std_string_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_std_string_utility_vector1_std_string_std_allocator_std_string_t (class in pyrosetta.rosetta.std) map_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_std_string_utility_vector1_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.std) map_string_to_torsion_bin_string() (in module pyrosetta.rosetta.core.conformation) map_symmetric_res_pairs() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) map_to_CEN() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) map_to_cen_atom_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) map_to_reference() (pyrosetta.rosetta.core.pose.toolbox.AtomID_Mapper method) map_torsion_bin_to_char() (in module pyrosetta.rosetta.core.conformation) map_unsigned_long_bool (class in pyrosetta.rosetta.std) map_unsigned_long_char (class in pyrosetta.rosetta.std) map_unsigned_long_core_conformation_symmetry_SymDof (class in pyrosetta.rosetta.std) map_unsigned_long_double (class in pyrosetta.rosetta.std) map_unsigned_long_numeric_xyzVector_double_t_std_allocator_std_pair_const_unsigned_long_numeric_xyzVector_double_t (class in pyrosetta.rosetta.std) map_unsigned_long_protocols_dna_DnaNeighbor (class in pyrosetta.rosetta.std) map_unsigned_long_protocols_dna_DnaPosition (class in pyrosetta.rosetta.std) map_unsigned_long_protocols_indexed_structure_store_FragmentLookupResult (class in pyrosetta.rosetta.std) map_unsigned_long_protocols_sewing_hashing_IdealContact (class in pyrosetta.rosetta.std) map_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t_std_allocator_std_pair_const_unsigned_long_std_map_core_chemical_AA_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_double_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_pair_char_std_string_t_std_allocator_std_pair_const_unsigned_long_std_pair_char_std_string_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_pair_double_double_t_std_allocator_std_pair_const_unsigned_long_std_pair_double_double_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_set_std_string_t_std_allocator_std_pair_const_unsigned_long_std_set_std_string_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_conformation_PseudoBondCollection_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_const_protocols_sewing_data_storage_LigandResidue_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_protocols_sewing_data_storage_LigandResidue_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_conformation_carbohydrates_GlycanTree_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_core_fragment_FragSet_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_fragment_FragSet_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_core_io_PositionDdGInfo_PositionDdGInfo_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_io_PositionDdGInfo_PositionDdGInfo_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_core_scoring_epr_deer_metrics_DEERData_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_core_scoring_epr_deer_metrics_DEERData_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_protocols_frags_TorsionFragmentLibrary_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frags_TorsionFragmentLibrary_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_indexed_structure_store_FragmentStore_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_LigandResidue_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_LigandResidue_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_SmartSegment_t_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_sewing_data_storage_SmartSegment_t (class in pyrosetta.rosetta.std) map_unsigned_long_std_string (class in pyrosetta.rosetta.std) map_unsigned_long_unsigned_long (class in pyrosetta.rosetta.std) map_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_core_id_AtomID_std_allocator_core_id_AtomID_t (class in pyrosetta.rosetta.std) map_unsigned_long_utility_vector1_double_std_allocator_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.std) map_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_bool_std_shared_ptr_core_conformation_Residue_std_allocator_std_pair_bool_std_shared_ptr_core_conformation_Residue_t (class in pyrosetta.rosetta.std) map_unsigned_long_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_numeric_xyzVector_double_double_std_allocator_std_pair_numeric_xyzVector_double_double_t (class in pyrosetta.rosetta.std) map_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t (class in pyrosetta.rosetta.std) map_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t (class in pyrosetta.rosetta.std) map_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_std_string_std_allocator_std_string_t (class in pyrosetta.rosetta.std) map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t_std_allocator_std_pair_const_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.std) mapfile_activated() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) MapHotspot (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) MapHotspotCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) mapping() (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) mapping_to_alignment() (in module pyrosetta.rosetta.core.sequence) maps_up_to_date() (pyrosetta.rosetta.core.chemical.ResidueTypeSetCache method) mapSphericalSamples() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) mapto() (pyrosetta.rosetta.core.scoring.constraints.Obsolet_NamedAtomPairConstraint method) maqw (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) maqx (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) maqy (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) maqz (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) mark() (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) mark_as_cancelled() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) mark_as_default() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) mark_as_finished() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) mark_as_invalid() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) mark_as_processed() (pyrosetta.rosetta.utility.SimulateMPIMessage method) mark_as_test_run() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) mark_atom_espGrid_points() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) mark_buried_solvent_points() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) mark_connect_incomplete() (pyrosetta.rosetta.core.conformation.Residue method) mark_connected() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) mark_current_job_id_for_repetition() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.BOINCJobDistributor method) (pyrosetta.rosetta.protocols.jd2.FileSystemJobDistributor 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) mark_designable() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) mark_disconnected() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) mark_energies_computed() (pyrosetta.rosetta.core.scoring.EnergyEdge method) mark_energies_uncomputed() (pyrosetta.rosetta.core.scoring.EnergyEdge method) mark_energy_computed() (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) mark_energy_uncomputed() (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingEnergyContainer method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfideEnergyContainer method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) mark_entity_as_unimportant() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) mark_incomplete() (pyrosetta.rosetta.core.chemical.ResConnID method) mark_last_entity_as_important() (pyrosetta.rosetta.protocols.pack_daemon.DaemonSet method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) mark_leave_as_is() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) mark_move_accepted() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator method) mark_move_rejected() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator method) mark_protein_espGrid_points() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) mark_residue_moved() (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) mark_structure_as_sampled() (pyrosetta.rosetta.protocols.features.StructureFeatures method) mark_tags() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) mark_thread_manager_as_initialized() (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManagerInitializationTracker method) mark_thread_manager_initialization_as_begun() (pyrosetta.rosetta.basic.thread_manager.RosettaThreadManagerInitializationTracker method) markDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) marked_for_deletion() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) markEdgeDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) markOneEdgeDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) markPocketDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) Martin (pyrosetta.rosetta.protocols.antibody.CDRDefinitionEnum attribute) marx (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) mary (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) marz (pyrosetta.rosetta.core.scoring.rna.chemical_shift.atomitem attribute) mask (pyrosetta.bindings.pose.PoseResidueLabelAccessor property) mask() (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) mask_asu() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) mask_for_element() (pyrosetta.rosetta.utility.DenseBoolMap_5_0_t static method) maskResidues() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) Mass (pyrosetta.rosetta.core.chemical.Element attribute) (pyrosetta.rosetta.core.chemical.Element.Properties attribute) mass (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) mass() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) MASTER (pyrosetta.rosetta.core.io.pdb.RecordType attribute) master() (pyrosetta.rosetta.core.conformation.ConformationKinWriter method) (pyrosetta.rosetta.core.conformation.ResidueKinWriter method) (pyrosetta.rosetta.protocols.match.output.ResidueKinemageWriter method) master_mover() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) MASTER_PROCESS_NEW_STRUCTURES (pyrosetta.rosetta.basic.ProfTag attribute) master_weight() (pyrosetta.rosetta.protocols.pose_metric_calculators.EnergiesData method) master_weight_vector() (pyrosetta.rosetta.protocols.pose_metric_calculators.DecomposeAndReweightEnergiesCalculator method) MasterFilter (class in pyrosetta.rosetta.protocols.constel) match() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) Match() (pyrosetta.rosetta.RDKit.Atom method) (pyrosetta.rosetta.RDKit.Bond method) match2D() (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) MATCH_AA (pyrosetta.rosetta.core.scoring.motif.MotifMatchOverlapReq attribute) match_aa1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) match_aa2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) MATCH_ALL (pyrosetta.rosetta.core.fragment.rna._RNA_MatchType_ attribute) MATCH_ANY (pyrosetta.rosetta.core.scoring.motif.MotifMatchOverlapReq attribute) match_chi_rmsd() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) match_dspos1 (class in pyrosetta.rosetta.protocols.match) MATCH_EXACT (pyrosetta.rosetta.core.fragment.rna._RNA_MatchType_ attribute) match_groups_dshits() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) match_groups_ushits() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) match_has_been_output() (pyrosetta.rosetta.protocols.match.MatchOutputTracker method) MATCH_HYDROPHOBICITY (pyrosetta.rosetta.core.scoring.motif.MotifMatchOverlapReq attribute) match_index (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookupResult property) match_lite_equals (class in pyrosetta.rosetta.protocols.match) match_lite_hasher (class in pyrosetta.rosetta.protocols.match) match_possible_for_hit_geometry() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) match_processing_successful() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) match_radius() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) match_res_mode() (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) match_rmsd (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookupResult property) match_rmsd_threshold (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookupResult property) MATCH_ROTAMER (pyrosetta.rosetta.core.scoring.motif.MotifMatchOverlapReq attribute) match_score (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookupResult property) match_score() (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) match_segments (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFGMSettings property) match_segments_ (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentSettings property) match_ss1() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) match_ss2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) match_template_and_target_sequence() (in module pyrosetta.rosetta.protocols.tcr) match_variants() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) MATCH_YR (pyrosetta.rosetta.core.fragment.rna._RNA_MatchType_ attribute) matchAtomFast() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) (pyrosetta.rosetta.protocols.loop_grower.DensSkeleton method) matchCentroidPose() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) MatchCollisionFilter (class in pyrosetta.rosetta.protocols.match.output) MatchConsolidator (class in pyrosetta.rosetta.protocols.match.output) MatchConstraintFileInfo (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) MatchConstraintFileInfoList (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) matchCount (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) MatchCounter (class in pyrosetta.rosetta.protocols.match) matched_residues_ (pyrosetta.rosetta.protocols.legacy_sewing.SewResidue property) matched_tags() (pyrosetta.rosetta.core.io.silent.SilentFileData method) Matcher (class in pyrosetta.rosetta.protocols.match) MatcherMover (class in pyrosetta.rosetta.protocols.match) MatcherMoverCreator (class in pyrosetta.rosetta.protocols.match) MatcherOutputStats (class in pyrosetta.rosetta.protocols.match) MatcherTask (class in pyrosetta.rosetta.protocols.match) matches() (pyrosetta.rosetta.core.io.ResidueInformation method) (pyrosetta.rosetta.core.scoring.constraints.CstEnergyContainer method) (pyrosetta.rosetta.protocols.topology_broker.ClaimerMessage method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer.CM_SuggestFixResidue method) (pyrosetta.rosetta.protocols.topology_broker.SuggestValueMessage method) matches_residue_type() (pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo method) (pyrosetta.rosetta.core.scoring.lkball.LKD_ResidueInfo method) MatchEvaluator (class in pyrosetta.rosetta.protocols.match.output) MatchFilter (class in pyrosetta.rosetta.protocols.match.output) MatchGrafter (class in pyrosetta.rosetta.protocols.metal_interface) MatchGrouper (class in pyrosetta.rosetta.protocols.match.output) MatchOutputter (class in pyrosetta.rosetta.protocols.match.output) MatchOutputTracker (class in pyrosetta.rosetta.protocols.match) matchPointFast() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) matchPose() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) matchPoseInPocket() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) MatchPositionModifier (class in pyrosetta.rosetta.protocols.match) MatchProcessor (class in pyrosetta.rosetta.protocols.match.output) matchRes() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) matchResFast() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) MatchResidues (class in pyrosetta.rosetta.protocols.fldsgn) MatchResiduesMover (class in pyrosetta.rosetta.protocols.fldsgn) MatchResiduesMoverCreator (class in pyrosetta.rosetta.protocols.fldsgn) MatchScoreWriter (class in pyrosetta.rosetta.protocols.match.output) MatDesGreedyOptMutationMover (class in pyrosetta.rosetta.protocols.matdes) MatDesGreedyOptMutationMoverCreator (class in pyrosetta.rosetta.protocols.matdes) MatDesPointMutationCalculator (class in pyrosetta.rosetta.protocols.matdes) MathMatrix_double_t (class in pyrosetta.rosetta.numeric) MathMatrix_float_t (class in pyrosetta.rosetta.numeric) MathNTensor_bool_3_t (class in pyrosetta.rosetta.numeric) MathNTensor_double_1_t (class in pyrosetta.rosetta.numeric) MathNTensor_double_2_t (class in pyrosetta.rosetta.numeric) MathNTensor_double_3_t (class in pyrosetta.rosetta.numeric) MathNTensor_double_4_t (class in pyrosetta.rosetta.numeric) MathNTensor_double_5_t (class in pyrosetta.rosetta.numeric) MathNTensor_double_6_t (class in pyrosetta.rosetta.numeric) MathNTensorBase_bool_t (class in pyrosetta.rosetta.numeric) MathNTensorBase_double_t (class in pyrosetta.rosetta.numeric) MathTensor_double_t (class in pyrosetta.rosetta.numeric) MathVector_double_t (class in pyrosetta.rosetta.numeric) MATRIX (pyrosetta.rosetta.protocols.cluster.calibur.ADJ_LIST_MODE attribute) matrix() (pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO method) (pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO method) matrix_finalized() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) matrix_initialized() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) MatrixMult() (in module pyrosetta.rosetta.numeric.model_quality) MatrixScoringScheme (class in pyrosetta.rosetta.core.sequence) MAX (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation attribute) max() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_bool_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_double_t method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) max_accepted_hbond_count() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) max_accepted_trials() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) max_allowed_oversaturated() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) max_angle() (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) max_angle_disp() (pyrosetta.rosetta.protocols.backrub.BackrubSegment method) max_angle_disp_4() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) max_angle_disp_7() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) max_angle_disp_slope() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) max_atom_radius() (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) max_atom_types() (pyrosetta.rosetta.core.scoring.packing.HolesParams method) max_atomic_interaction_cutoff() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) max_atomic_interaction_distance() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) max_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) max_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) max_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) max_bucket_count() (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) max_ca_dis2() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) max_cache_size() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) max_calpha_distance() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) max_cb_cb_dist() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) max_clash_score (pyrosetta.rosetta.protocols.sewing.hashing.HasherSettings property) MAX_CLASS (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.QualityClass attribute) max_connpoints_for_residue() (pyrosetta.rosetta.core.scoring.trie.CPDataCorrespondence method) max_contacts (pyrosetta.rosetta.protocols.sewing.hashing.IdealContact property) max_context_neighbor_cutoff() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) max_cycles() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) max_dis (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) max_dis() (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondPotential method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc method) (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_dis2() (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_dist() (pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) max_dist_squared() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker method) max_dist_to_center() (pyrosetta.rosetta.core.conformation.UltraLightResidue method) max_distance (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.ConstraintConditions property) max_distance() (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerValueRange method) max_donated_hbond_count() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) max_frag_len() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) max_frag_length() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) max_gap_percentage() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) max_generations() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) max_hb_energy() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) max_heavy_heavy_cutoff() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_heavy_hydrogen_cutoff() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_hydrogen_hydrogen_cutoff() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_hydrogen_lj_radius() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_inner_cycles() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) max_insertion_length (pyrosetta.rosetta.protocols.indexed_structure_store.DirectSegmentLookupConfig property) max_inter_ss_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) max_intra_ss_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) max_iter() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.optimization.MinimizerOptions method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) max_length() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) max_linear_chainbreak() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) max_load_factor() (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) max_missing_weight() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) max_network_size() (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) max_noe_distance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) max_non_hydrogen_lj_radius() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_nstruct() (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) max_nstruct_index() (in module pyrosetta.rosetta.protocols.jd2) max_ntries() (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen method) max_ntries_ (pyrosetta.rosetta.protocols.stepwise.StepWiseSampleAndScreen property) max_num_results() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) max_number_mutations_ (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric property) max_occurs (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary property) max_occurs() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) max_path_length() (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) max_per_move_torsion_delta_per_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) max_pools() (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) max_population_size() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) max_pos() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) MAX_PROBABILITY (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2.ScoreType attribute) max_rad() (in module pyrosetta.rosetta.core.scoring.packstat) max_rama_score_increase() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase method) max_residue_count() (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) max_rms() (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) max_rmsd_in_region() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) max_rot_per_trans_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) max_rotbump_energy() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) max_rounds() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) max_sample_iterations() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.BaseTabooPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.NeighborDependentTorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TabooSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionRestrictedKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSweepingKinematicPerturber method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.VicinitySamplingKinematicPerturber method) max_samples() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) max_sasa() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapDatabase method) max_sasa_score (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.BlockParam property) max_score() (pyrosetta.rosetta.core.scoring.motif.XformScore method) max_score_diffs() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) max_segments() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementSet method) max_separation_dist_to_target_atom() (pyrosetta.rosetta.protocols.match.downstream.AtomAngleSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDihedralSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomDistanceSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.AtomGeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.GeometrySecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.ScoringSecMatchRPE method) (pyrosetta.rosetta.protocols.match.downstream.SecMatchResiduePairEvaluator method) max_seq_sep() (pyrosetta.rosetta.protocols.constraints_additional.MaxSeqSepConstraintSet method) max_size() (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.io.Remarks method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.std.multimap_double_std_pair_unsigned_long_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStubSet_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t method) (pyrosetta.rosetta.std.multimap_double_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t method) (pyrosetta.rosetta.std.set_core_chemical_gasteiger_GasteigerAtomTypeData_AtomicOrbitalTypes_t method) (pyrosetta.rosetta.std.set_core_id_DOF_ID_t method) (pyrosetta.rosetta.std.set_core_id_PartialAtomID_t method) (pyrosetta.rosetta.std.set_double_t method) (pyrosetta.rosetta.std.set_int_t method) (pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.std.set_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.set_std_shared_ptr_protocols_environment_ClientMover_t method) (pyrosetta.rosetta.std.set_std_string_t method) (pyrosetta.rosetta.std.set_unsigned_long_t method) (pyrosetta.rosetta.std.unordered_map_basic_datacache_ResRotPair_float_basic_datacache_ResRotPairHasher_std_equal_to_basic_datacache_ResRotPair_std_allocator_std_pair_const_basic_datacache_ResRotPair_float_t method) (pyrosetta.rosetta.std.unordered_map_std_pair_char_char_int_core_sequence_CharPairHash_std_equal_to_std_pair_char_char_std_allocator_std_pair_const_std_pair_char_char_int_t method) (pyrosetta.rosetta.std.unordered_map_unsigned_long_numeric_MathMatrix_float_t method) (pyrosetta.rosetta.std.vector_core_io_AtomInformation method) (pyrosetta.rosetta.std.vector_core_io_RemarkInfo method) (pyrosetta.rosetta.std.vector_core_pose_Pose method) (pyrosetta.rosetta.std.vector_core_scoring_hbonds_graph_HBondInfo method) (pyrosetta.rosetta.std.vector_core_scoring_sc__DOT method) (pyrosetta.rosetta.std.vector_core_scoring_sc_Atom method) (pyrosetta.rosetta.std.vector_double method) (pyrosetta.rosetta.std.vector_float method) (pyrosetta.rosetta.std.vector_int method) (pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.vector_protocols_cluster_Cluster method) (pyrosetta.rosetta.std.vector_protocols_motif_grafting_movers_MotifMatch method) (pyrosetta.rosetta.std.vector_RDGeom_Point3D method) (pyrosetta.rosetta.std.vector_RDKit_Dict_Pair method) (pyrosetta.rosetta.std.vector_std_list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_pair_std_shared_ptr_protocols_filters_Filter_protocols_filters_boolean_operations_t method) (pyrosetta.rosetta.std.vector_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_std_list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.vector_std_string method) (pyrosetta.rosetta.std.vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_int_t method) 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(pyrosetta.rosetta.utility.vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Column method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_ForeignKey method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Index method) (pyrosetta.rosetta.utility.vector1_basic_sampling_orientations_QuatDBMetadata method) (pyrosetta.rosetta.utility.vector1_bool method) (pyrosetta.rosetta.utility.vector1_char method) (pyrosetta.rosetta.utility.vector1_const_utility_vector1_int_std_allocator_int__star_t method) (pyrosetta.rosetta.utility.vector1_core_chemical_AA method) (pyrosetta.rosetta.utility.vector1_core_chemical_Adduct method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomICoor method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomType method) (pyrosetta.rosetta.utility.vector1_core_chemical_BondName method) (pyrosetta.rosetta.utility.vector1_core_chemical_io_merge_residue_behavior method) (pyrosetta.rosetta.utility.vector1_core_chemical_MutableResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_exposed_hydrophobic_data method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondEdge method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packing_Ball method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_Sphere method) (pyrosetta.rosetta.utility.vector1_core_scoring_power_diagram_SAnode method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmallAtNb method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_tableID method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_Point method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_RocPoint method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_backbone_moves_local_backbone_mover_Residue method) (pyrosetta.rosetta.utility.vector1_protocols_backrub_BackrubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef1 method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef2 method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_DataPoint method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_Exemplar method) (pyrosetta.rosetta.utility.vector1_protocols_constraints_additional_ConstraintEvaluator method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_StructureSlice method) (pyrosetta.rosetta.utility.vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_hybridization_detailedControlsTagSetting method) (pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub method) (pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSelector_JumpWeightDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_ResTorsions method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_SheetPositions method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_RotData method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_monte_carlo_AcceptedScores method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_nonlocal_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_MutationData method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_MergePDBMover_Overlap method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_qsar_ColorGradient method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_recces_Histogram method) (pyrosetta.rosetta.utility.vector1_protocols_relax_DatabaseRelaxScript method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_RegionalConnections method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_IonizableResidue method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_LoggedFragmentMover_Item method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_WaterRot method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_std_string_std_string_std_allocator_std_pair_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_double_std_allocator_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_std_allocator_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_set_protocols_match_downstream_hit_std_less_protocols_match_downstream_hit_std_allocator_protocols_match_downstream_hit_std_allocator_std_set_protocols_match_downstream_hit_std_less_protocols_match_downstream_hit_std_allocator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_std_allocator_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_std_allocator_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_std_allocator_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_std_allocator_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_kinematics_tree_Atom_std_allocator_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_optimization_DOF_Node_std_allocator_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_interaction_graph_NPDHBond_std_allocator_std_shared_ptr_core_pack_interaction_graph_NPDHBond_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_task_ResfileCommand_std_allocator_std_shared_ptr_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_scoring_saxs_DistanceHistogram_std_allocator_std_shared_ptr_core_scoring_saxs_DistanceHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_sequence_Cell_std_allocator_std_shared_ptr_core_sequence_Cell_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_antibody_PDBLandmark_std_allocator_std_shared_ptr_protocols_antibody_PDBLandmark_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_std_allocator_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_std_allocator_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_jd3_JGJobNode_std_allocator_std_shared_ptr_protocols_jd3_JGJobNode_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_std_allocator_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_std_allocator_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_std_allocator_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_std_allocator_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_std_allocator_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_std_allocator_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) max_size_col() (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) max_step_limit_ (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization property) max_strands() (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) max_struct() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) max_struct_try() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) max_temperature() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) max_terminal_length_ (pyrosetta.rosetta.protocols.pose_sewing.movers.SeedSettings property) max_total_torsion_delta_per_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) max_trials() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) max_tries() (pyrosetta.rosetta.protocols.moves.FilterMover method) max_tries_multiplier_for_ccd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) MAX_TYPE (pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE attribute) max_val() (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.numeric.Polynomial_1d method) max_valence_electrons_sp() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) max_value() (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) max_values() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) max_volume_contribution() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) max_weight_ (pyrosetta.rosetta.protocols.optimize_weights.WeightRangeConstraint property) MaxAngularMomentumQuantumNumber (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration.AngularMomentumQuantumNumber attribute) maxcall (pyrosetta.rosetta.numeric.nls.lm_control_struct property) maxcycles() (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) maxd2 (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) maxDiff (pyrosetta.tests.bindings.core.test_pose.TestPoseIO attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent attribute) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs attribute) MaxExpression (class in pyrosetta.rosetta.numeric.expression_parser) maximum_value() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) maxiter (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams property) maxNominalRes() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) MaxPrincipleQuantumNumber (pyrosetta.rosetta.core.chemical.ElectronConfiguration attribute) (pyrosetta.rosetta.core.chemical.ElectronConfiguration.PrincipalQuantumNumber attribute) maxrad() (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGrid method) MaxSeqSepConstraintSet (class in pyrosetta.rosetta.protocols.constraints_additional) maxsub (pyrosetta.rosetta.core.scoring.TMscoreStore property) maxsub_max (pyrosetta.rosetta.core.scoring.TMscoreStore property) maxsub_sum (pyrosetta.rosetta.core.scoring.TMscoreStore property) maxtrials() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) may_change_aa() (pyrosetta.rosetta.core.chemical.AddAtom method) (pyrosetta.rosetta.core.chemical.AddAtomAlias method) (pyrosetta.rosetta.core.chemical.AddBond method) (pyrosetta.rosetta.core.chemical.AddBondType method) (pyrosetta.rosetta.core.chemical.AddChi method) (pyrosetta.rosetta.core.chemical.AddChiRotamer method) (pyrosetta.rosetta.core.chemical.AddConnect method) (pyrosetta.rosetta.core.chemical.AddConnectAndTrackingVirt method) (pyrosetta.rosetta.core.chemical.AddConnectDeleteChildProton method) (pyrosetta.rosetta.core.chemical.AddProperty method) (pyrosetta.rosetta.core.chemical.AddProtonChi method) (pyrosetta.rosetta.core.chemical.AppendMainchainAtom method) (pyrosetta.rosetta.core.chemical.ChangeAncestory method) (pyrosetta.rosetta.core.chemical.ChangeBondType method) (pyrosetta.rosetta.core.chemical.ChiralFlipAtoms method) (pyrosetta.rosetta.core.chemical.ChiralFlipNaming method) (pyrosetta.rosetta.core.chemical.ClearChiRotamers method) (pyrosetta.rosetta.core.chemical.ConnectSulfurAndMakeVirtualProton method) (pyrosetta.rosetta.core.chemical.DeleteActCoordAtom method) (pyrosetta.rosetta.core.chemical.DeleteAtom method) (pyrosetta.rosetta.core.chemical.DeleteChildProton method) (pyrosetta.rosetta.core.chemical.DeleteMetalbindingAtom method) (pyrosetta.rosetta.core.chemical.DeleteProperty method) (pyrosetta.rosetta.core.chemical.DeleteTerminalChi method) (pyrosetta.rosetta.core.chemical.DeleteVariantType method) (pyrosetta.rosetta.core.chemical.NCAARotLibBBTorsions method) (pyrosetta.rosetta.core.chemical.NCAARotLibNumRotamerBins method) (pyrosetta.rosetta.core.chemical.NCAARotLibPath method) (pyrosetta.rosetta.core.chemical.PatchCase method) (pyrosetta.rosetta.core.chemical.PatchOperation method) (pyrosetta.rosetta.core.chemical.PrependMainchainAtom method) (pyrosetta.rosetta.core.chemical.RamaPreproFilename method) (pyrosetta.rosetta.core.chemical.RamaPreproResname method) (pyrosetta.rosetta.core.chemical.RedefineChi method) (pyrosetta.rosetta.core.chemical.RemoveRotamerSpecifications method) (pyrosetta.rosetta.core.chemical.RenameAtom method) (pyrosetta.rosetta.core.chemical.ReplaceMainchainAtom method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithBromine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithChlorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithEthyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithFluorine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithHydroxyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithIodine method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethoxy method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithMethyl method) (pyrosetta.rosetta.core.chemical.ReplaceProtonWithTrifluoromethyl method) (pyrosetta.rosetta.core.chemical.ResetBondLength method) (pyrosetta.rosetta.core.chemical.Set_AA method) (pyrosetta.rosetta.core.chemical.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetBaseName method) (pyrosetta.rosetta.core.chemical.SetDisulfideAtomName method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius method) (pyrosetta.rosetta.core.chemical.SetNetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetOrientAtom method) (pyrosetta.rosetta.core.chemical.SetPolymerConnectAtom method) (pyrosetta.rosetta.core.chemical.SetVirtualShadow method) (pyrosetta.rosetta.core.chemical.VirtualizeAll method) (pyrosetta.rosetta.core.chemical.VirtualizeSidechain method) maybe_init() (in module pyrosetta.distributed) maybe_initialize_handler() (in module pyrosetta.logging_support) Mbhbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) mc() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) MC() (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MixedMonteCarlo method) mc() (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) MC_ACCEPT (pyrosetta.rosetta.basic.ProfTag attribute) mc_accepted() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) mc_accepted_string() (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) mc_accpeted() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) MC_Any (class in pyrosetta.rosetta.protocols.recces.sampler) MC_ANY (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) MC_Comb (class in pyrosetta.rosetta.protocols.recces.sampler) MC_COMB (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) MC_Loop (class in pyrosetta.rosetta.protocols.recces.sampler) MC_LOOP (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) MC_ONE_TORSION (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) MC_OneTorsion (class in pyrosetta.rosetta.protocols.recces.sampler) MC_RNA_KIC (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) MC_RNA_KIC_Sampler (class in pyrosetta.rosetta.protocols.recces.sampler.rna) MC_RNA_MULTI_SUITE (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) MC_RNA_MultiSuite (class in pyrosetta.rosetta.protocols.recces.sampler.rna) MC_RNA_ONE_JUMP (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) MC_RNA_OneJump (class in pyrosetta.rosetta.protocols.recces.sampler.rna) MC_RNA_Sugar (class in pyrosetta.rosetta.protocols.recces.sampler.rna) MC_RNA_SUGAR (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) MC_RNA_Suite (class in pyrosetta.rosetta.protocols.recces.sampler.rna) MC_RNA_SUITE (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) MC_Sampler (class in pyrosetta.rosetta.protocols.recces.sampler) MCA (class in pyrosetta.rosetta.protocols.moves) MCA_accepted_score_beat_last (pyrosetta.rosetta.protocols.moves.MCA attribute) MCA_accepted_score_beat_low (pyrosetta.rosetta.protocols.moves.MCA attribute) MCA_accepted_thermally (pyrosetta.rosetta.protocols.moves.MCA attribute) MCA_rejected (pyrosetta.rosetta.protocols.moves.MCA attribute) MCAligner (class in pyrosetta.rosetta.core.sequence) Mcbeta (pyrosetta.rosetta.core.scoring.ScoreType attribute) mCen (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) mcfi() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) mcfi_list() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) mcfi_lists_size() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) mCluCen (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) mcm_cycles (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) MCSAligner (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) MCSAlignerOptions (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) MCShowMover (class in pyrosetta.rosetta.protocols.moves) Md (pyrosetta.rosetta.core.chemical.element.Elements attribute) mD2C (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) MD_Angle (class in pyrosetta.rosetta.protocols.cartesian) MD_Bond (class in pyrosetta.rosetta.protocols.cartesian) md_energy_report_stepsize() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) MD_HarmonicDihedral (class in pyrosetta.rosetta.protocols.cartesian) md_report_stepsize() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) md_rsr_update_stepsize() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) MDBase (class in pyrosetta.rosetta.protocols.md) MDLTYP (pyrosetta.rosetta.core.io.pdb.RecordType attribute) mdsch() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) MDscheduleData (class in pyrosetta.rosetta.protocols.md) Mean (class in pyrosetta.rosetta.protocols.pack_daemon) MEAN (pyrosetta.rosetta.core.scoring.nmr.NMR_VALUE_AVERAGING_TYPE attribute) mean (pyrosetta.rosetta.core.simple_metrics.metrics.summary_type attribute) mean() (in module pyrosetta.rosetta.numeric) mean_and_stdev() (in module pyrosetta.rosetta.protocols.mpi_refinement) MEAN_FIELD (pyrosetta.rosetta.basic.ProfTag attribute) MEAN_PROBABILITY (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2.ScoreType attribute) mean_sd (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData property) mean_squared_error() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) MeanField (class in pyrosetta.rosetta.protocols.mean_field) MeanFieldFactory (class in pyrosetta.rosetta.protocols.mean_field) measure (pyrosetta.rosetta.core.io.CisPeptideInformation property) measure_bp_specificities() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) measure_rotamer_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBins method) measure_sequence_recovery() (pyrosetta.rosetta.protocols.pose_metric_calculators.SequenceComparison method) measure_sp3acc_BAH_from_hvy() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) measure_specificities() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) measure_specificity() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) MED_AMBIG (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.QualityClass attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D attribute) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.QualityClass attribute) Medal_main() (in module pyrosetta.rosetta.protocols.medal) MedalExchange_main() (in module pyrosetta.rosetta.protocols.medal) MedalExchangeMover (class in pyrosetta.rosetta.protocols.medal) MedalMover (class in pyrosetta.rosetta.protocols.medal) median (pyrosetta.rosetta.core.scoring.sc.ShapeSimilarityCalculator property) median() (in module pyrosetta.rosetta.numeric) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) median_ (pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t property) meets_requirements() (pyrosetta.rosetta.core.chemical.Metapatch method) MEM (class in pyrosetta.rosetta.core.conformation.membrane) mem_all_atom_rmsd_no_super() (in module pyrosetta.rosetta.protocols.membrane) mem_all_atom_rmsd_with_super() (in module pyrosetta.rosetta.protocols.membrane) mem_bb_rmsd_no_super() (in module pyrosetta.rosetta.protocols.membrane) mem_bb_rmsd_with_super() (in module pyrosetta.rosetta.protocols.membrane) mem_cbeta_2TM_den12() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_2TM_den6() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_4TM_den12() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_4TM_den6() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_den12() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_cbeta_den6() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_env_log10() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_env_log6() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_foot_print() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMap method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) mem_footprint() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct 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.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) mem_pair_log() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) mem_stats() (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) memb_dsolv1() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_dsolv2() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_etable() (pyrosetta.rosetta.core.scoring.ScoringManager method) memb_lk_dgfree() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_lk_dgrefce() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_solv1() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_solv2() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) MembAccesResidueLipophilicityFilter (class in pyrosetta.rosetta.protocols.simple_filters) MembAccesResidueLipophilicityFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) Membed_init() (pyrosetta.rosetta.core.scoring.MembranePotential method) member (pyrosetta.rosetta.protocols.cluster.Cluster property) Member() (pyrosetta.rosetta.basic.sampling.orientations.Permute method) member() (pyrosetta.rosetta.numeric.DiscreteIntervalEncodingTree_unsigned_long_t method) member_constraints() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) MembEtable (class in pyrosetta.rosetta.core.scoring.etable) MEMBRANE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) membrane() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) membrane_axis() (in module pyrosetta.rosetta.protocols.membrane) membrane_center() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_core() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) MEMBRANE_EMBED (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) Membrane_FAEmbed (class in pyrosetta.rosetta.core.scoring) MEMBRANE_FAEMBED (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) Membrane_FAEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) Membrane_FAPotential (class in pyrosetta.rosetta.core.scoring) membrane_from_topology() (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) membrane_geometry() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_info() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) membrane_jump() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_normal() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_normal_to_length_15() (in module pyrosetta.rosetta.protocols.membrane) membrane_rsd_num() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_span_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) membrane_span_term_z_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) membrane_steepness() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_thickness() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) MEMBRANE_TOPOLOGY (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) MembraneAbinitio (class in pyrosetta.rosetta.protocols.abinitio) MembraneAbinitio.StageID (class in pyrosetta.rosetta.protocols.abinitio) MembraneCbetaEnergy (class in pyrosetta.rosetta.core.energy_methods) MembraneCbetaEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MembraneCenPairEnergy (class in pyrosetta.rosetta.core.energy_methods) MembraneCenPairEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MembraneCenterPerturbationMover (class in pyrosetta.rosetta.protocols.rigid) MembraneData (class in pyrosetta.rosetta.core.scoring.membrane) MembraneEmbed (class in pyrosetta.rosetta.core.scoring) MembraneEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) MembraneEnergyLandscapeSampler (class in pyrosetta.rosetta.protocols.membrane_benchmark) MembraneEnergyLandscapeSamplerCreator (class in pyrosetta.rosetta.protocols.membrane_benchmark) MembraneEnvEnergy (class in pyrosetta.rosetta.core.energy_methods) MembraneEnvEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MembraneEnvPenalties (class in pyrosetta.rosetta.core.energy_methods) MembraneEnvPenaltiesCreator (class in pyrosetta.rosetta.core.energy_methods) MembraneEnvSmoothEnergy (class in pyrosetta.rosetta.core.energy_methods) MembraneEnvSmoothEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MembraneGeometry (class in pyrosetta.rosetta.core.conformation.membrane) MembraneInfo (class in pyrosetta.rosetta.core.conformation.membrane) MembraneJump (class in pyrosetta.rosetta.protocols.jumping) MembraneLipo (class in pyrosetta.rosetta.core.energy_methods) MembraneLipoCreator (class in pyrosetta.rosetta.core.energy_methods) MembraneNormalPerturbationMover (class in pyrosetta.rosetta.protocols.rigid) MembranePositionFromTopologyMover (class in pyrosetta.rosetta.protocols.membrane) MembranePositionFromTopologyMoverCreator (class in pyrosetta.rosetta.protocols.membrane) MembranePotential (class in pyrosetta.rosetta.core.scoring) MembraneSpanConstraint (class in pyrosetta.rosetta.core.scoring.constraints) MembraneSpanConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) MembraneSpanConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) MembraneSpanTermZConstraint (class in pyrosetta.rosetta.core.scoring.constraints) MembraneTopology (class in pyrosetta.rosetta.core.scoring) (class in pyrosetta.rosetta.protocols.simple_moves) MembraneTopology_from_pose() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) MembraneTopologyClaimer (class in pyrosetta.rosetta.protocols.topology_broker) MembraneTopologyCreator (class in pyrosetta.rosetta.protocols.simple_moves) memory_usage_in_bytes() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) memory_use() (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) MemTracer (class in pyrosetta.rosetta.basic) MemTracer.TracerProxy (class in pyrosetta.rosetta.basic) MemTracerImpl (class in pyrosetta.rosetta.basic) MemTracerImpl.sentry (class in pyrosetta.rosetta.basic) MemTracerImpl.TracerProxyImpl (class in pyrosetta.rosetta.basic) MemTracerImpl.TracerProxyImpl.sentry (class in pyrosetta.rosetta.basic) Menv (pyrosetta.rosetta.core.scoring.ScoreType attribute) Menv_non_helix (pyrosetta.rosetta.core.scoring.ScoreType attribute) Menv_penalties() (pyrosetta.rosetta.core.scoring.MembranePotential method) Menv_smooth (pyrosetta.rosetta.core.scoring.ScoreType attribute) Menv_termini (pyrosetta.rosetta.core.scoring.ScoreType attribute) Menv_tm_proj (pyrosetta.rosetta.core.scoring.ScoreType attribute) MEnvAtomParams (class in pyrosetta.rosetta.protocols.membrane.scoring) merge() (in module pyrosetta.rosetta.protocols.forge.methods) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) merge_bbdb() (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) merge_before() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) merge_behavior_for_name3() (pyrosetta.rosetta.core.chemical.io.MergeAndSplitBehaviorManager method) merge_chains() (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) merge_constraints_from_cmdline() (in module pyrosetta.rosetta.core.scoring.constraints) merge_constraints_from_cmdline_to_pose() (in module pyrosetta.rosetta.core.scoring.constraints) merge_constraints_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.constraints) merge_data() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) merge_fa_constraints_from_cmdline() (in module pyrosetta.rosetta.core.scoring.constraints) merge_fa_constraints_from_cmdline_to_pose() (in module pyrosetta.rosetta.core.scoring.constraints) merge_fa_constraints_from_cmdline_to_scorefxn() (in module pyrosetta.rosetta.core.scoring.constraints) merge_frags() (in module pyrosetta.rosetta.core.fragment) merge_in_other_pose() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_in_other_pose_by_bond() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_in_other_pose_by_jump() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_junction_sequence() (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) merge_poses() (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) merge_residue_behavior (class in pyrosetta.rosetta.core.chemical.io) merge_segments() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) merge_split_behavior_manager() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) merge_two_poses() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_two_poses_using_full_model_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler) merge_vectors() (in module pyrosetta.rosetta.protocols.stepwise.modeler) mergeable() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) MergeAndSplitBehaviorManager (class in pyrosetta.rosetta.core.chemical.io) merged() (pyrosetta.rosetta.utility.options.OptionCollection static method) MergePDBatOverlapMover (class in pyrosetta.rosetta.protocols.pose_creation) MergePDBatOverlapMoverCreator (class in pyrosetta.rosetta.protocols.pose_creation) MergePDBMover (class in pyrosetta.rosetta.protocols.pose_creation) MergePDBMover.Overlap (class in pyrosetta.rosetta.protocols.pose_creation) MergePDBMoverCreator (class in pyrosetta.rosetta.protocols.pose_creation) meridian_angle_degrees_ (pyrosetta.rosetta.protocols.legacy_sewing.Model property) MessageListener (class in pyrosetta.rosetta.basic.mpi) MessageListenerFactory (class in pyrosetta.rosetta.basic.mpi) messages_for_node() (pyrosetta.rosetta.utility.SimulateMPIData method) messages_from_node() (pyrosetta.rosetta.utility.SimulateMPIData method) META_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) METAL (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) metal_bond_angle_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) metal_bond_dist_constraint_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) metal_bond_LJ_multiplier() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) Metal_HelperBase (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) Metal_HelperBase_Metal (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) Metal_HelperBase_MetalLigand (class in pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker) metal_type() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) metal_type_string() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) METALBINDING (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) metalbinding_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) metalbinding_constraint_energy() (pyrosetta.rosetta.core.scoring.constraints.ConstraintEdge method) MetalContactsConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) MetalContactsConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.constraint_generator) metalhash_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) MetalloClaimer (class in pyrosetta.rosetta.protocols.topology_broker) MetalSiteResidue (class in pyrosetta.rosetta.protocols.metal_interface) MetaMaxExpression (class in pyrosetta.rosetta.numeric.expression_parser) MetaMinExpression (class in pyrosetta.rosetta.numeric.expression_parser) Metapatch (class in pyrosetta.rosetta.core.chemical) metapatch() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) metapatch_map() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) MetapatchEnumeration (class in pyrosetta.rosetta.protocols.residue_optimization) metapatches() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) MetaPoseEvaluator (class in pyrosetta.rosetta.protocols.evaluation) MetaPoseInputStream (class in pyrosetta.rosetta.core.import_pose.pose_stream) method_type() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) method_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) methodname() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) MethodParams (class in pyrosetta.rosetta.protocols.mpi_refinement) methods (pyrosetta.CD property)

methods_picked() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) METHYL (pyrosetta.rosetta.protocols.noesy_assign.CALIBRATION_ATOM_TYPE attribute) METHYL_GLYCOSIDE (pyrosetta.rosetta.core.chemical.VariantType attribute) METHYL_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) METHYLATED_CTERMINUS (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) METHYLATED_CTERMINUS_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) METHYLATED_NA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) METHYLATED_NTERM_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) METHYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) MethylNameLibrary (class in pyrosetta.rosetta.protocols.noesy_assign) MethylNames (class in pyrosetta.rosetta.protocols.noesy_assign) metric() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) metric_ (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric property) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric property) metric_data() (pyrosetta.rosetta.protocols.jd3.job_summaries.StandardPoseJobSummary method) metric_for_evaluation() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) metric_labels (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep property) metric_value() (pyrosetta.rosetta.protocols.multistate_design.SingleStateEntityData method) metric_value_map() (pyrosetta.rosetta.protocols.multistate_design.SingleStateEntityData method) metric_value_template() (pyrosetta.rosetta.protocols.pose_metric_calculators.MetricValueGetter method) MetricCalculatorFitnessFunction (class in pyrosetta.rosetta.protocols.multistate_design) MetricData (class in pyrosetta.rosetta.protocols.features) MetricKey (class in pyrosetta.rosetta.core.simple_metrics) MetricRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) MetricRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) metrics (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep property) MetricValueBase (class in pyrosetta.rosetta.basic) MetricValueGetter (class in pyrosetta.rosetta.protocols.pose_metric_calculators) metropolis_hastings_mover() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) MetropolisHastingsMover (class in pyrosetta.rosetta.protocols.canonical_sampling) MetropolisHastingsMoverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) mFinalClusters (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) mFinalDecoy (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) Mg (pyrosetta.rosetta.core.chemical.element.Elements attribute) mg (pyrosetta.rosetta.core.scoring.ScoreType attribute) MG2_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) mg_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) mg_coord_cst_dist() (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) mg_lig (pyrosetta.rosetta.core.scoring.ScoreType attribute) mg_pair_nblist (pyrosetta.rosetta.core.scoring.min_pair_data attribute) mg_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) mg_res() (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) mg_sol (pyrosetta.rosetta.core.scoring.ScoreType attribute) MgEnergy (class in pyrosetta.rosetta.core.energy_methods) MgEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MgHydrater (class in pyrosetta.rosetta.protocols.magnesium) MgKnowledgeBasedPotential (class in pyrosetta.rosetta.core.scoring.magnesium) MgMinimizer (class in pyrosetta.rosetta.protocols.magnesium) MgMonteCarlo (class in pyrosetta.rosetta.protocols.magnesium) MgOrbitalFrameFinder (class in pyrosetta.rosetta.protocols.magnesium) MgScanner (class in pyrosetta.rosetta.protocols.magnesium) MgWaterHydrogenPacker (class in pyrosetta.rosetta.protocols.magnesium) MH_end_of_list (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_Metal attribute) MH_Fe2 (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_Metal attribute) MH_Ni2 (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_Metal attribute) MH_unknown_metal (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_Metal attribute) MH_Zn (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_Metal attribute) mhc_epitope (pyrosetta.rosetta.core.scoring.ScoreType attribute) mhc_epitope_energy_setup() (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) mhc_epitope_setup_file() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) mhc_epitope_setup_file_count() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) MHCEpitopeConstraint (class in pyrosetta.rosetta.core.scoring.mhc_epitope_energy) MHCEpitopeEnergy (class in pyrosetta.rosetta.core.energy_methods) MHCEpitopeEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MHCEpitopeEnergySetup (class in pyrosetta.rosetta.core.scoring.mhc_epitope_energy) MHCEpitopePredictor (class in pyrosetta.rosetta.core.scoring.mhc_epitope_energy) MHCEpitopePredictorExternal (class in pyrosetta.rosetta.core.scoring.mhc_epitope_energy) MHCEpitopePredictorMatrix (class in pyrosetta.rosetta.core.scoring.mhc_epitope_energy) MHCEpitopePredictorPreLoaded (class in pyrosetta.rosetta.core.scoring.mhc_epitope_energy) MHCEpitopePredictorSVM (class in pyrosetta.rosetta.core.scoring.mhc_epitope_energy) MHLigand_end_of_list (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand attribute) MHLigand_N_pyridine (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand attribute) MHLigand_Nd_histidine (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand attribute) MHLigand_Ne_histidine (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand attribute) MHLigand_O_carboxyl (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand attribute) MHLigand_S_cysteine (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand attribute) MHLigand_unknown_ligand (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase_MetalLigand attribute) mid_pos() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Base method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) middle_res() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) MidPhiOut (class in pyrosetta.rosetta.protocols.frag_picker.scores) midpoint() (pyrosetta.rosetta.protocols.loops.Loop method) MidPsiOut (class in pyrosetta.rosetta.protocols.frag_picker.scores) MIN (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation attribute) min() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.id.DOF_ID_Range method) (pyrosetta.rosetta.core.id.TorsionID_Range method) (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.MathNTensor_bool_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_1_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_2_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_3_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_4_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_5_t method) (pyrosetta.rosetta.numeric.MathNTensor_double_6_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_bool_t method) (pyrosetta.rosetta.numeric.MathNTensorBase_double_t method) (pyrosetta.rosetta.numeric.random.RandomGenerator method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) min_ (pyrosetta.rosetta.numeric.ClusterOptions property) min_angle() (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) min_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) MIN_AVG_DIST_BASED (pyrosetta.rosetta.protocols.cluster.calibur.EST_THRESHOLD_MODE attribute) min_bb() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_bb_set() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) min_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) min_c_terminal_charges() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) min_cav_ball_radius (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) min_client_rank() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) min_cluster_overlap (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) min_contribution_symmetric_peaks_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) min_dis() (pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc method) (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) min_dis2() (pyrosetta.rosetta.core.scoring.etable.coulomb.Coulomb method) (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) min_dist() (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) (pyrosetta.rosetta.protocols.noesy_assign.FragsToAtomDist.DistanceRecord method) min_distance() (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) min_frag_length() (pyrosetta.rosetta.protocols.splice.RotLibOut method) min_hash_score (pyrosetta.rosetta.protocols.sewing.hashing.HasherSettings property) min_heap() (pyrosetta.rosetta.protocols.cluster.Exemplar static method) min_helix_length() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) min_hole_radius (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) min_i_ (pyrosetta.rosetta.numeric.ClusterOptions property) min_inter_ss_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) min_intra_ss_bbrms() (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) min_j_ (pyrosetta.rosetta.numeric.ClusterOptions property) min_len_helix() (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) min_len_strand() (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) min_length() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) min_loop_size() (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) min_max() (in module pyrosetta.rosetta.core.scoring.epr_deer) min_mod() (in module pyrosetta.rosetta.protocols.cryst) min_mover() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) min_n_terminal_charges() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) min_neighbor_sc() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) min_occurs (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary property) min_occurs() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) min_only (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) min_options() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) min_or_max_occurs_set (pyrosetta.rosetta.utility.tag.XMLSchemaSimpleSubelementList.ElementSummary property) min_pack() (in module pyrosetta.rosetta.core.pack) min_pack_min_element() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) min_pack_optimize() (in module pyrosetta.rosetta.core.pack) min_pack_place_opt_rotamers_on_pose() (in module pyrosetta.rosetta.core.pack) min_pack_setup() (in module pyrosetta.rosetta.core.pack) min_pair_data (class in pyrosetta.rosetta.core.scoring) min_pair_data_type() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) min_pos() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) MIN_PROBABILITY (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2.ScoreType attribute) min_rb() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_rb_set() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_receptor_bb (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) min_residue_count() (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) min_rms() (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) min_sc() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_sc_set() (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) min_seg() (in module pyrosetta.rosetta.protocols.splice) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) min_segments() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementSet method) min_seq_sep (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.ConstraintConditions property) min_seq_sep() (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) min_seq_separation_residue_assignment() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) min_single_data (class in pyrosetta.rosetta.core.scoring) min_single_data_type() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) min_solution_count() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) min_symm_dist2() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) min_temperature() (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator method) min_terminal_length_ (pyrosetta.rosetta.protocols.pose_sewing.movers.SeedSettings property) min_tolerance() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) min_type() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.optimization.MinimizerOptions method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) min_type_enum_to_string() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) min_type_is_present() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) min_type_string_to_enum() (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignEnumManager method) min_val() (pyrosetta.rosetta.core.scoring.hbonds.Polynomial_1d method) (pyrosetta.rosetta.numeric.Polynomial_1d method) min_value() (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) min_VC_to_write() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) min_volume_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) min_weight_ (pyrosetta.rosetta.protocols.optimize_weights.WeightRangeConstraint property) minAtomRingSize() (pyrosetta.rosetta.RDKit.RingInfo method) minBondRingSize() (pyrosetta.rosetta.RDKit.RingInfo method) MinExpression (class in pyrosetta.rosetta.numeric.expression_parser) mini_pose() (pyrosetta.rosetta.core.import_pose.libraries.ChunkSet method) mini_pose_list() (pyrosetta.rosetta.core.import_pose.libraries.BasePairStepLibrary method) minima (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType attribute) MinimalClashHash (class in pyrosetta.rosetta.numeric.geometry.hashing) MinimalFragSet (class in pyrosetta.rosetta.core.fragment) MinimalFragSetIterator_ (class in pyrosetta.rosetta.core.fragment) MinimalistFlexbbEdge (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) MinimalistFlexbbInteractionGraph (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) MinimalistFlexbbInteractionGraph.Subsitution (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) MinimalistFlexbbNode (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) MinimalRotamer (class in pyrosetta.rosetta.protocols.minimization_packing) minimization_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) minimization_score_function() (pyrosetta.rosetta.protocols.ddg.ddGMover method) minimization_threshold() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) minimization_type() (pyrosetta.rosetta.protocols.mainchain_potential.GenerateMainchainPotentialOptions method) MinimizationEdge (class in pyrosetta.rosetta.core.scoring) MinimizationGraph (class in pyrosetta.rosetta.core.scoring) MinimizationNode (class in pyrosetta.rosetta.core.scoring) MinimizationRefiner (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) MinimizationRefinerCreator (class in pyrosetta.rosetta.protocols.loop_modeling.refiners) minimize (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum attribute) minimize() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) minimize_after_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) minimize_all() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) minimize_all_protein() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) minimize_all_rotamers() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) minimize_and_score_native_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) minimize_and_score_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) minimize_backbone() (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder method) minimize_bond_angles() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) minimize_bond_lengths() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) minimize_bps() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) minimize_cartesian (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum attribute) minimize_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) minimize_conformation() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) minimize_during_scoring() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) minimize_flexible_region() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) minimize_in_stages() (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) minimize_in_whole_structure_context() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) minimize_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) minimize_ligand_ (pyrosetta.rosetta.protocols.ligand_docking.LigandArea property) minimize_magnesium_and_hydration_shell() (in module pyrosetta.rosetta.protocols.magnesium) minimize_mg_coord_constraint_distance() (pyrosetta.rosetta.protocols.magnesium.MgScanner method) minimize_no_bb() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) minimize_overlap() (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) minimize_pose() (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) minimize_poseOP_into_density() (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) minimize_protein() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) minimize_protein_sc() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) minimize_region() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) minimize_rotamer() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) minimize_rounds() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) minimize_scorefxn() (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) minimize_segment() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) minimize_single_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) minimize_single_res_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) minimize_structure() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) minimize_sumsq() (in module pyrosetta.rosetta.core.scoring.epr_deer) minimize_sumsq_nodim() (in module pyrosetta.rosetta.core.scoring.epr_deer) minimize_tcr_model() (in module pyrosetta.rosetta.protocols.tcr) minimize_tolerance() (pyrosetta.rosetta.core.optimization.MinimizerOptions method) minimize_toward_stub() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) minimize_w_pre_csts() (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) minimize_waters() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) minimize_with_constraints() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) MinimizeBackbone (class in pyrosetta.rosetta.protocols.ligand_docking) MinimizeBackboneCreator (class in pyrosetta.rosetta.protocols.ligand_docking) MinimizeHotspots() (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot method) MinimizeInterface() (in module pyrosetta.rosetta.protocols.protein_interface_design) MinimizeLigand (class in pyrosetta.rosetta.protocols.ligand_docking) MinimizePoseIntoDensityOptions (class in pyrosetta.rosetta.protocols.electron_density) Minimizer (class in pyrosetta.rosetta.core.optimization) minimizer_loop() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) minimizer_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) minimizer_options() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) minimizer_rename_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) minimizer_use_coordinate_constraints() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) MinimizerMap (class in pyrosetta.rosetta.core.optimization) MinimizerMapBase (class in pyrosetta.rosetta.core.kinematics) MinimizerMode (class in pyrosetta.rosetta.protocols.stepwise.modeler) MinimizerOptions (class in pyrosetta.rosetta.core.optimization) MinimizeStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) minimum_bounding_ellipse() (in module pyrosetta.rosetta.numeric.linear_algebra) minimum_hbond_energy() (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) minimum_peak_intensity() (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) minimum_sampling_probability() (pyrosetta.rosetta.core.scoring.Ramachandran method) (pyrosetta.rosetta.core.scoring.Ramachandran2B method) minimum_value() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) MinimumInterAlphaDistanceMetric (class in pyrosetta.rosetta.protocols.pose_sewing.simple_metrics) MinimumInterAlphaDistanceMetricCreator (class in pyrosetta.rosetta.protocols.pose_sewing.simple_metrics) MiniPose (class in pyrosetta.rosetta.core.pose) MiniRelax (class in pyrosetta.rosetta.protocols.relax) MinMover (class in pyrosetta.rosetta.protocols.minimization_packing) MINMOVER_APPLY (pyrosetta.rosetta.basic.ProfTag attribute) MinMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) minmult() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) MinMultiHarmonicFunc (class in pyrosetta.rosetta.core.scoring.func) minor_radius() (pyrosetta.rosetta.numeric.linear_algebra.EllipseParameters method) MinPackMover (class in pyrosetta.rosetta.protocols.minimization_packing) MinPackMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) mInputFileName (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) MinScoreScoreFunction (class in pyrosetta.rosetta.core.scoring) mintolerance() (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) mintype() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) MinTypeEnum (class in pyrosetta.rosetta.protocols.antibody.design) MinTypeEnum_total (pyrosetta.rosetta.protocols.antibody.design.MinTypeEnum attribute) mirror_backbone_dihedrals (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) mirror_symm() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) mirror_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) mirror_z() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryTransform method) mirrored_relative_to_type() (pyrosetta.rosetta.core.conformation.Residue method) MirrorSymmetricConformation (class in pyrosetta.rosetta.core.conformation.symmetry) mismatch_score() (pyrosetta.rosetta.core.sequence.SimpleScoringScheme method) misplaced() (pyrosetta.rosetta.core.conformation.Residue method) missing_atoms() (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) missing_dens_as_jump() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) missing_in_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstParamCache method) missing_res (pyrosetta.rosetta.core.scoring.ScoreType attribute) missing_residues() (pyrosetta.rosetta.core.scoring.loop_graph.LoopGraph method) MissingDensityToJumpMover (class in pyrosetta.rosetta.protocols.simple_moves) MissingEnergy (class in pyrosetta.rosetta.core.energy_methods) MissingEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) mixed_disulfide() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) MIXED_t (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) MixedMonteCarlo (class in pyrosetta.rosetta.protocols.moves) MixtureFunc (class in pyrosetta.rosetta.core.scoring.func) mk_neigh_list() (in module pyrosetta.rosetta.protocols.constel) MKDIR() (in module pyrosetta.rosetta.protocols.sparta) mkdir_pred() (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib method) mLen (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) Mlipo (pyrosetta.rosetta.core.scoring.ScoreType attribute) mm() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) mm_atom_name() (pyrosetta.rosetta.core.conformation.Residue method) mm_atom_set() (pyrosetta.rosetta.core.scoring.mm.MMLJLibrary method) mm_atom_type() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom method) mm_atom_type_index() (pyrosetta.rosetta.core.chemical.ResidueType method) mm_atom_type_name() (pyrosetta.rosetta.core.chemical.Adduct method) mm_atom_type_set() (pyrosetta.rosetta.core.chemical.ChemicalManager method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) mm_atom_types_ptr() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) mm_bend (pyrosetta.rosetta.core.scoring.ScoreType attribute) mm_bond_angle_residue_type_param_set() (in module pyrosetta.rosetta.core.scoring.mm) mm_bondangle_library() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleResidueTypeParamSet method) mm_disable (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) mm_enable (pyrosetta.rosetta.core.select.movemap.move_map_action attribute) mm_from_residues() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) mm_lj_energy_inter_method (pyrosetta.rosetta.core.scoring.methods.EnergyMethods attribute) mm_lj_inter_atr (pyrosetta.rosetta.core.scoring.ScoreType attribute) MM_LJ_INTER_NBLIST (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) mm_lj_inter_rep (pyrosetta.rosetta.core.scoring.ScoreType attribute) mm_lj_intra_atr (pyrosetta.rosetta.core.scoring.ScoreType attribute) mm_lj_intra_atr_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) MM_LJ_INTRA_NBLIST (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) mm_lj_intra_nblist (pyrosetta.rosetta.core.scoring.min_single_data attribute) mm_lj_intra_rep (pyrosetta.rosetta.core.scoring.ScoreType attribute) mm_lj_intra_rep_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) mm_lj_library() (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) mm_lj_score() (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) MM_LJ_TRIE_COLLECTION (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) mm_name() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) mm_stretch (pyrosetta.rosetta.core.scoring.ScoreType attribute) mm_twist (pyrosetta.rosetta.core.scoring.ScoreType attribute) mm_twist_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) mm_type() (pyrosetta.rosetta.core.conformation.Atom method) (pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom method) (pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom method) MMAtomType (class in pyrosetta.rosetta.core.chemical) MMAtomTypeSet (class in pyrosetta.rosetta.core.chemical) MMBondAngleEnergy (class in pyrosetta.rosetta.core.scoring.methods) MMBondAngleEnergyCreator (class in pyrosetta.rosetta.core.scoring.methods) MMBondAngleLibrary (class in pyrosetta.rosetta.core.scoring.mm) MMBondAngleResidueTypeParam (class in pyrosetta.rosetta.core.scoring.mm) MMBondAngleResidueTypeParamSet (class in pyrosetta.rosetta.core.scoring.mm) MMBondAngleScore (class in pyrosetta.rosetta.core.scoring.mm) MMBondLengthEnergy (class in pyrosetta.rosetta.core.scoring.methods) MMBondLengthEnergyCreator (class in pyrosetta.rosetta.core.scoring.methods) MMBondLengthLibrary (class in pyrosetta.rosetta.core.scoring.mm) MMBondLengthScore (class in pyrosetta.rosetta.core.scoring.mm) mmCIFJobOutputter (class in pyrosetta.rosetta.protocols.jd2) mmCIFJobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) mmCIFParser (class in pyrosetta.rosetta.core.chemical.mmCIF) MMEnergyTableAtom (class in pyrosetta.rosetta.core.scoring.mm.mmtrie) mmf() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) mmf_cat_in_datamap() (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader static method) mmf_ct_namer() (pyrosetta.rosetta.core.select.movemap.MoveMapFactory static method) mmf_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader static method) MMLJEnergyInter (class in pyrosetta.rosetta.core.scoring.methods) MMLJEnergyInterCreator (class in pyrosetta.rosetta.core.scoring.methods) MMLJEnergyIntra (class in pyrosetta.rosetta.core.scoring.methods) MMLJEnergyIntraCreator (class in pyrosetta.rosetta.core.scoring.methods) MMLJEnergyTable (class in pyrosetta.rosetta.core.scoring.mm) MMLJLibrary (class in pyrosetta.rosetta.core.scoring.mm) MMLJScore (class in pyrosetta.rosetta.core.scoring.mm) mmtf_extra_data_io() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) MMTF_file (pyrosetta.rosetta.core.import_pose.FileType attribute) mmtfJobOutputter (class in pyrosetta.rosetta.protocols.jd2) mmtfJobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) mmTFPoseOutputSpecification (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) mmTFPoseOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) mmTFPoseOutputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) MMTorsionEnergy (class in pyrosetta.rosetta.core.scoring.methods) MMTorsionEnergyCreator (class in pyrosetta.rosetta.core.scoring.methods) MMTorsionLibrary (class in pyrosetta.rosetta.core.scoring.mm) MMTorsionScore (class in pyrosetta.rosetta.core.scoring.mm) Mn (pyrosetta.rosetta.core.chemical.element.Elements attribute) MN2_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) MNBRAK() (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) mNumDecoy (pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB property) mnx_ (pyrosetta.rosetta.core.scoring.packstat.Octree2D property) mny_ (pyrosetta.rosetta.core.scoring.packstat.Octree2D property) Mo (pyrosetta.rosetta.core.chemical.element.Elements attribute) mod() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.numeric.ModSelector_long_true_t static method) (pyrosetta.rosetta.numeric.ModSelector_unsigned_long_true_t static method) (pyrosetta.rosetta.ObjexxFCL.ModSelector_int_true_t static method) mode() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.normalmode.NormalMode method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) mode1_1_packertask() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) mode1_packertask() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) mode2_packertask() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) mode3_packertask() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) mode4_packertask() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) mode5_packertask() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) mode6_packertask() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) mode_ (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator property) mode_enum_from_name() (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric static method) mode_name_from_enum() (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric static method) Model (class in pyrosetta.rosetta.protocols.legacy_sewing) MODEL (pyrosetta.rosetta.core.io.pdb.RecordType attribute) model() (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) model_count() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) model_file_from_options() (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) model_h3() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) model_id (pyrosetta.rosetta.protocols.legacy_sewing.Basis property) (pyrosetta.rosetta.protocols.legacy_sewing.HashValue property) model_id() (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) model_id_ (pyrosetta.rosetta.protocols.legacy_sewing.Model property) (pyrosetta.rosetta.protocols.legacy_sewing.SewSegment property) model_ids() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) model_index (pyrosetta.rosetta.core.io.mmtf.sd_index property) model_name_ (pyrosetta.rosetta.protocols.esm_perplexity.EsmPerplexityTensorflowProtocol property) model_resnum() (pyrosetta.rosetta.protocols.legacy_sewing.HashEdge method) model_tag() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) model_with_density() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoPoseInitializer method) modeler_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) modeler_sugar_at_chain_break() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) modeler_sugar_at_five_prime() (in module pyrosetta.rosetta.protocols.stepwise.sampler.rna) modeler_sugar_at_three_prime() (in module pyrosetta.rosetta.protocols.stepwise.sampler.rna) ModelFeatures (class in pyrosetta.rosetta.protocols.features) ModelFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ModelFileReader (class in pyrosetta.rosetta.protocols.sewing.hashing) ModelNode (class in pyrosetta.rosetta.protocols.legacy_sewing) models() (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) modeltag() (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pose.PDBInfo method) modifiable() (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.moves.ResId method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) modifiable_residue_type_set_for_conf() (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) modification() (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) modified2original_interval_endpoints() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) MODIFIED_DDG (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2.ScoreType attribute) modified_match_positions() (pyrosetta.rosetta.protocols.match.AddAllPositionsMPM method) (pyrosetta.rosetta.protocols.match.BfactorMPM method) (pyrosetta.rosetta.protocols.match.MatchPositionModifier method) (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) (pyrosetta.rosetta.protocols.match.RemoveNorCTermMPM method) (pyrosetta.rosetta.protocols.match.SecondaryStructureMPM method) (pyrosetta.rosetta.protocols.match.TaskOperationMPM method) modified_task() (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) modifieddensity() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) ModifiedResidueInformation (class in pyrosetta.rosetta.core.io) modifiedscore() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) modify() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) modify_after_jump() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) modify_atom_properties_from_command_line() (in module pyrosetta.rosetta.core.chemical) modify_before_jump() (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) modify_dbase_with_compatible_backbones() (in module pyrosetta.rosetta.protocols.splice) modify_foldtree() (pyrosetta.rosetta.protocols.splice.RBInMover method) modify_ft_for_residue_insertion() (in module pyrosetta.rosetta.protocols.denovo_design.components) modify_impl() (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) modify_pdb_segments_with_current_segment() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) modify_pose_build_resids_from_endes_input() (pyrosetta.rosetta.protocols.match.MatcherTask method) modify_relative_filters_pdb_names() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) modify_task() (pyrosetta.rosetta.core.pack.task.TaskFactory method) modify_unselected_residues() (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) MODIFY_WAS_SUCCESSFUL (pyrosetta.rosetta.protocols.forge.build.BuildInstructionState.Enum attribute) modify_was_successful() (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) ModifyAnnealer (class in pyrosetta.rosetta.protocols.task_operations) ModifyAnnealerCreator (class in pyrosetta.rosetta.protocols.task_operations) ModifyStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) ModifyVariantTypeMover (class in pyrosetta.rosetta.protocols.simple_moves) ModifyVariantTypeMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) modp() (in module pyrosetta.rosetta.numeric.kinematic_closure) MODRES (pyrosetta.rosetta.core.io.pdb.RecordType attribute) modres_map() (pyrosetta.rosetta.core.io.StructFileRep method) modrf() (in module pyrosetta.rosetta.numeric.kinematic_closure) ModSelector_int_true_t (class in pyrosetta.rosetta.ObjexxFCL) ModSelector_long_true_t (class in pyrosetta.rosetta.numeric) ModSelector_unsigned_long_true_t (class in pyrosetta.rosetta.numeric) module pyrosetta pyrosetta.bindings pyrosetta.bindings.energies pyrosetta.bindings.homogeneous_transform pyrosetta.bindings.pose pyrosetta.bindings.rt pyrosetta.bindings.utility pyrosetta.distributed pyrosetta.distributed.dask pyrosetta.distributed.docs pyrosetta.distributed.io pyrosetta.distributed.packed_pose pyrosetta.distributed.packed_pose.core pyrosetta.distributed.tasks pyrosetta.distributed.utility pyrosetta.distributed.utility.pickle pyrosetta.io pyrosetta.io.silent_file_map pyrosetta.logging_support pyrosetta.network pyrosetta.network.rosetta_udp_to_tcp_bridge pyrosetta.numeric pyrosetta.numeric.alignment pyrosetta.protocols pyrosetta.protocols.h5_fragment_store_provider pyrosetta.protocols.h5_importer pyrosetta.protocols.h5_structure_store_provider pyrosetta.rosetta pyrosetta.rosetta.basic pyrosetta.rosetta.basic.citation_manager pyrosetta.rosetta.basic.database pyrosetta.rosetta.basic.database.insert_statement_generator pyrosetta.rosetta.basic.database.schema_generator pyrosetta.rosetta.basic.datacache pyrosetta.rosetta.basic.gpu pyrosetta.rosetta.basic.mpi pyrosetta.rosetta.basic.options pyrosetta.rosetta.basic.random pyrosetta.rosetta.basic.resource_manager pyrosetta.rosetta.basic.resource_manager.locator pyrosetta.rosetta.basic.sampling pyrosetta.rosetta.basic.sampling.orientations pyrosetta.rosetta.basic.svd pyrosetta.rosetta.basic.tensorflow_manager pyrosetta.rosetta.basic.thread_manager pyrosetta.rosetta.core pyrosetta.rosetta.core.chemical pyrosetta.rosetta.core.chemical.bcl pyrosetta.rosetta.core.chemical.carbohydrates pyrosetta.rosetta.core.chemical.element pyrosetta.rosetta.core.chemical.gasteiger pyrosetta.rosetta.core.chemical.io pyrosetta.rosetta.core.chemical.mainchain_potential pyrosetta.rosetta.core.chemical.mmCIF pyrosetta.rosetta.core.chemical.modifications pyrosetta.rosetta.core.chemical.NucleotideTools pyrosetta.rosetta.core.chemical.orbitals pyrosetta.rosetta.core.chemical.rdkit pyrosetta.rosetta.core.chemical.rings pyrosetta.rosetta.core.chemical.rna pyrosetta.rosetta.core.chemical.rotamers pyrosetta.rosetta.core.chemical.sdf pyrosetta.rosetta.core.conformation pyrosetta.rosetta.core.conformation.carbohydrates pyrosetta.rosetta.core.conformation.membrane pyrosetta.rosetta.core.conformation.membrane.membrane_geometry pyrosetta.rosetta.core.conformation.orbitals pyrosetta.rosetta.core.conformation.parametric pyrosetta.rosetta.core.conformation.residue_datacache pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType pyrosetta.rosetta.core.conformation.signals pyrosetta.rosetta.core.conformation.symmetry pyrosetta.rosetta.core.energy_methods pyrosetta.rosetta.core.energy_methods.dfire pyrosetta.rosetta.core.environment pyrosetta.rosetta.core.enzymes pyrosetta.rosetta.core.fragment pyrosetta.rosetta.core.fragment.picking_old pyrosetta.rosetta.core.fragment.picking_old.concepts pyrosetta.rosetta.core.fragment.picking_old.vall pyrosetta.rosetta.core.fragment.picking_old.vall.eval pyrosetta.rosetta.core.fragment.picking_old.vall.gen pyrosetta.rosetta.core.fragment.picking_old.vall.scores pyrosetta.rosetta.core.fragment.rna pyrosetta.rosetta.core.grid pyrosetta.rosetta.core.id pyrosetta.rosetta.core.import_pose pyrosetta.rosetta.core.import_pose.atom_tree_diffs pyrosetta.rosetta.core.import_pose.libraries pyrosetta.rosetta.core.import_pose.options pyrosetta.rosetta.core.import_pose.pose_stream pyrosetta.rosetta.core.init pyrosetta.rosetta.core.io pyrosetta.rosetta.core.io.carbohydrates pyrosetta.rosetta.core.io.external pyrosetta.rosetta.core.io.mmcif pyrosetta.rosetta.core.io.mmtf pyrosetta.rosetta.core.io.nmr pyrosetta.rosetta.core.io.pdb pyrosetta.rosetta.core.io.pose_from_sfr pyrosetta.rosetta.core.io.pose_to_sfr pyrosetta.rosetta.core.io.PositionDdGInfo pyrosetta.rosetta.core.io.raw_data pyrosetta.rosetta.core.io.rcsb pyrosetta.rosetta.core.io.rna pyrosetta.rosetta.core.io.sequence_comparation pyrosetta.rosetta.core.io.serialization pyrosetta.rosetta.core.io.silent pyrosetta.rosetta.core.kinematics pyrosetta.rosetta.core.kinematics.inverse pyrosetta.rosetta.core.kinematics.jacobian pyrosetta.rosetta.core.kinematics.tree pyrosetta.rosetta.core.membrane pyrosetta.rosetta.core.optimization pyrosetta.rosetta.core.optimization.symmetry pyrosetta.rosetta.core.pack pyrosetta.rosetta.core.pack.annealer pyrosetta.rosetta.core.pack.dunbrack pyrosetta.rosetta.core.pack.dunbrack.cenrot pyrosetta.rosetta.core.pack.guidance_scoreterms pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome pyrosetta.rosetta.core.pack.guidance_scoreterms.sap pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy pyrosetta.rosetta.core.pack.hbonds pyrosetta.rosetta.core.pack.interaction_graph pyrosetta.rosetta.core.pack.palette pyrosetta.rosetta.core.pack.rotamer_set pyrosetta.rosetta.core.pack.rotamer_set.symmetry pyrosetta.rosetta.core.pack.rotamers pyrosetta.rosetta.core.pack.scmin pyrosetta.rosetta.core.pack.task pyrosetta.rosetta.core.pack.task.operation pyrosetta.rosetta.core.pack.task.residue_selector pyrosetta.rosetta.core.pack.task.rna pyrosetta.rosetta.core.pack_basic pyrosetta.rosetta.core.pose pyrosetta.rosetta.core.pose.carbohydrates pyrosetta.rosetta.core.pose.copydofs pyrosetta.rosetta.core.pose.datacache pyrosetta.rosetta.core.pose.full_model_info pyrosetta.rosetta.core.pose.metrics pyrosetta.rosetta.core.pose.metrics.simple_calculators pyrosetta.rosetta.core.pose.motif pyrosetta.rosetta.core.pose.ncbb pyrosetta.rosetta.core.pose.reference_pose pyrosetta.rosetta.core.pose.rna pyrosetta.rosetta.core.pose.rna.secstruct_legacy pyrosetta.rosetta.core.pose.signals pyrosetta.rosetta.core.pose.symmetry pyrosetta.rosetta.core.pose.toolbox pyrosetta.rosetta.core.scoring pyrosetta.rosetta.core.scoring.aa_composition_energy pyrosetta.rosetta.core.scoring.annealing pyrosetta.rosetta.core.scoring.atomic_depth pyrosetta.rosetta.core.scoring.bin_transitions pyrosetta.rosetta.core.scoring.carbohydrates pyrosetta.rosetta.core.scoring.carbon_hbonds pyrosetta.rosetta.core.scoring.constraints pyrosetta.rosetta.core.scoring.cryst pyrosetta.rosetta.core.scoring.custom_pair_distance pyrosetta.rosetta.core.scoring.disulfides pyrosetta.rosetta.core.scoring.dna pyrosetta.rosetta.core.scoring.dssp pyrosetta.rosetta.core.scoring.elec pyrosetta.rosetta.core.scoring.elec.electrie pyrosetta.rosetta.core.scoring.electron_density pyrosetta.rosetta.core.scoring.electron_density_atomwise pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType pyrosetta.rosetta.core.scoring.epr_deer pyrosetta.rosetta.core.scoring.epr_deer.metrics pyrosetta.rosetta.core.scoring.etable pyrosetta.rosetta.core.scoring.etable.coulomb pyrosetta.rosetta.core.scoring.etable.count_pair pyrosetta.rosetta.core.scoring.etable.etrie pyrosetta.rosetta.core.scoring.facts pyrosetta.rosetta.core.scoring.fiber_diffraction pyrosetta.rosetta.core.scoring.func pyrosetta.rosetta.core.scoring.geometric_solvation pyrosetta.rosetta.core.scoring.hbonds pyrosetta.rosetta.core.scoring.hbonds.graph pyrosetta.rosetta.core.scoring.hbonds.hbtrie pyrosetta.rosetta.core.scoring.interface_ pyrosetta.rosetta.core.scoring.lkball pyrosetta.rosetta.core.scoring.lkball.lkbtrie pyrosetta.rosetta.core.scoring.loop_graph pyrosetta.rosetta.core.scoring.loop_graph.evaluator pyrosetta.rosetta.core.scoring.magnesium pyrosetta.rosetta.core.scoring.membrane pyrosetta.rosetta.core.scoring.methods pyrosetta.rosetta.core.scoring.methods.dfire pyrosetta.rosetta.core.scoring.mhc_epitope_energy pyrosetta.rosetta.core.scoring.mm pyrosetta.rosetta.core.scoring.mm.mmtrie pyrosetta.rosetta.core.scoring.motif pyrosetta.rosetta.core.scoring.netcharge_energy pyrosetta.rosetta.core.scoring.nmr pyrosetta.rosetta.core.scoring.nmr.pcs pyrosetta.rosetta.core.scoring.nmr.pre pyrosetta.rosetta.core.scoring.nmr.rdc pyrosetta.rosetta.core.scoring.nv pyrosetta.rosetta.core.scoring.orbitals pyrosetta.rosetta.core.scoring.packing pyrosetta.rosetta.core.scoring.packstat pyrosetta.rosetta.core.scoring.packstat.old pyrosetta.rosetta.core.scoring.power_diagram pyrosetta.rosetta.core.scoring.rna pyrosetta.rosetta.core.scoring.rna.chemical_shift pyrosetta.rosetta.core.scoring.rna.data pyrosetta.rosetta.core.scoring.sasa pyrosetta.rosetta.core.scoring.saxs pyrosetta.rosetta.core.scoring.sc pyrosetta.rosetta.core.scoring.solid_surface pyrosetta.rosetta.core.scoring.sym_e pyrosetta.rosetta.core.scoring.symmetry pyrosetta.rosetta.core.scoring.trie pyrosetta.rosetta.core.scoring.vdwaals pyrosetta.rosetta.core.select pyrosetta.rosetta.core.select.jump_selector pyrosetta.rosetta.core.select.movemap pyrosetta.rosetta.core.select.residue_selector pyrosetta.rosetta.core.select.residue_selector.slice_enums pyrosetta.rosetta.core.select.util pyrosetta.rosetta.core.sequence pyrosetta.rosetta.core.simple_metrics pyrosetta.rosetta.core.simple_metrics.composite_metrics pyrosetta.rosetta.core.simple_metrics.metrics pyrosetta.rosetta.core.simple_metrics.per_residue_metrics pyrosetta.rosetta.core.util pyrosetta.rosetta.cppdb pyrosetta.rosetta.cppdb.backend pyrosetta.rosetta.numeric pyrosetta.rosetta.numeric.alignment pyrosetta.rosetta.numeric.conversions pyrosetta.rosetta.numeric.crick_equations pyrosetta.rosetta.numeric.expression_parser pyrosetta.rosetta.numeric.fourier pyrosetta.rosetta.numeric.geometry pyrosetta.rosetta.numeric.geometry.hashing pyrosetta.rosetta.numeric.histograms pyrosetta.rosetta.numeric.interpolation pyrosetta.rosetta.numeric.interpolation.spline pyrosetta.rosetta.numeric.kdtree pyrosetta.rosetta.numeric.kinematic_closure pyrosetta.rosetta.numeric.kinematic_closure.radians pyrosetta.rosetta.numeric.linear_algebra pyrosetta.rosetta.numeric.model_quality pyrosetta.rosetta.numeric.nls pyrosetta.rosetta.numeric.random pyrosetta.rosetta.numeric.statistics pyrosetta.rosetta.ObjexxFCL pyrosetta.rosetta.ObjexxFCL.bit pyrosetta.rosetta.ObjexxFCL.format pyrosetta.rosetta.ObjexxFCL.Fortran pyrosetta.rosetta.ObjexxFCL.internal pyrosetta.rosetta.ObjexxFCL.internal.ObserverMediator pyrosetta.rosetta.protocols pyrosetta.rosetta.protocols.aa_composition pyrosetta.rosetta.protocols.abinitio pyrosetta.rosetta.protocols.abinitio.abscript pyrosetta.rosetta.protocols.analysis pyrosetta.rosetta.protocols.analysis.burial_metrics pyrosetta.rosetta.protocols.analysis.simple_metrics pyrosetta.rosetta.protocols.anchored_design pyrosetta.rosetta.protocols.antibody pyrosetta.rosetta.protocols.antibody.clusters pyrosetta.rosetta.protocols.antibody.constraints pyrosetta.rosetta.protocols.antibody.design pyrosetta.rosetta.protocols.antibody.grafting pyrosetta.rosetta.protocols.antibody.residue_selector pyrosetta.rosetta.protocols.antibody.snugdock pyrosetta.rosetta.protocols.antibody.task_operations pyrosetta.rosetta.protocols.antibody_legacy pyrosetta.rosetta.protocols.backbone_moves pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers pyrosetta.rosetta.protocols.backrub pyrosetta.rosetta.protocols.branch_angle pyrosetta.rosetta.protocols.buns pyrosetta.rosetta.protocols.calc_taskop_filters pyrosetta.rosetta.protocols.calc_taskop_movers pyrosetta.rosetta.protocols.canonical_sampling pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks pyrosetta.rosetta.protocols.carbohydrates pyrosetta.rosetta.protocols.cartesian pyrosetta.rosetta.protocols.checkpoint pyrosetta.rosetta.protocols.chemically_conjugated_docking pyrosetta.rosetta.protocols.chemistries pyrosetta.rosetta.protocols.chromophore pyrosetta.rosetta.protocols.cluster pyrosetta.rosetta.protocols.cluster.calibur pyrosetta.rosetta.protocols.comparative_modeling pyrosetta.rosetta.protocols.comparative_modeling.features pyrosetta.rosetta.protocols.constel pyrosetta.rosetta.protocols.constraint_filters pyrosetta.rosetta.protocols.constraint_generator pyrosetta.rosetta.protocols.constraint_movers pyrosetta.rosetta.protocols.constraints_additional pyrosetta.rosetta.protocols.contact_map pyrosetta.rosetta.protocols.coupled_moves pyrosetta.rosetta.protocols.cryst pyrosetta.rosetta.protocols.cutoutdomain pyrosetta.rosetta.protocols.cyclic_peptide pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker pyrosetta.rosetta.protocols.cyclic_peptide_predict pyrosetta.rosetta.protocols.ddG pyrosetta.rosetta.protocols.ddg pyrosetta.rosetta.protocols.ddg.CartesianddG pyrosetta.rosetta.protocols.denovo_design pyrosetta.rosetta.protocols.denovo_design.architects pyrosetta.rosetta.protocols.denovo_design.calculators pyrosetta.rosetta.protocols.denovo_design.components pyrosetta.rosetta.protocols.denovo_design.connection pyrosetta.rosetta.protocols.denovo_design.constraints pyrosetta.rosetta.protocols.denovo_design.filters pyrosetta.rosetta.protocols.denovo_design.movers pyrosetta.rosetta.protocols.denovo_design.residue_selectors pyrosetta.rosetta.protocols.denovo_design.task_operations pyrosetta.rosetta.protocols.design_opt pyrosetta.rosetta.protocols.dna pyrosetta.rosetta.protocols.dna_dock pyrosetta.rosetta.protocols.docking pyrosetta.rosetta.protocols.docking.membrane pyrosetta.rosetta.protocols.docking.stateless pyrosetta.rosetta.protocols.domain_assembly pyrosetta.rosetta.protocols.drug_design pyrosetta.rosetta.protocols.drug_design.bcl pyrosetta.rosetta.protocols.electron_density pyrosetta.rosetta.protocols.energy_based_clustering pyrosetta.rosetta.protocols.environment pyrosetta.rosetta.protocols.environment.claims pyrosetta.rosetta.protocols.enzdes pyrosetta.rosetta.protocols.enzdes.enzutil pyrosetta.rosetta.protocols.enzymatic_movers pyrosetta.rosetta.protocols.esm_perplexity pyrosetta.rosetta.protocols.evaluation pyrosetta.rosetta.protocols.evolution pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools pyrosetta.rosetta.protocols.farnesyl pyrosetta.rosetta.protocols.features pyrosetta.rosetta.protocols.features.helixAssembly pyrosetta.rosetta.protocols.features.RelevantResiduesMode pyrosetta.rosetta.protocols.features.strand_assembly pyrosetta.rosetta.protocols.fibril pyrosetta.rosetta.protocols.filters pyrosetta.rosetta.protocols.fldsgn pyrosetta.rosetta.protocols.fldsgn.filters pyrosetta.rosetta.protocols.fldsgn.potentials pyrosetta.rosetta.protocols.fldsgn.potentials.sspot pyrosetta.rosetta.protocols.fldsgn.topology pyrosetta.rosetta.protocols.flexpack pyrosetta.rosetta.protocols.flexpack.annealer pyrosetta.rosetta.protocols.flexpack.interaction_graph pyrosetta.rosetta.protocols.flexpack.rotamer_set pyrosetta.rosetta.protocols.flexpep_docking pyrosetta.rosetta.protocols.floppy_tail pyrosetta.rosetta.protocols.flxbb pyrosetta.rosetta.protocols.fold_from_loops pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator pyrosetta.rosetta.protocols.fold_from_loops.filters pyrosetta.rosetta.protocols.fold_from_loops.movers pyrosetta.rosetta.protocols.fold_from_loops.selectors pyrosetta.rosetta.protocols.fold_from_loops.utils pyrosetta.rosetta.protocols.forge pyrosetta.rosetta.protocols.forge.build pyrosetta.rosetta.protocols.forge.build.BuildInstructionState pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme pyrosetta.rosetta.protocols.forge.components pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage pyrosetta.rosetta.protocols.forge.constraints pyrosetta.rosetta.protocols.forge.methods pyrosetta.rosetta.protocols.forge.remodel pyrosetta.rosetta.protocols.frag_picker pyrosetta.rosetta.protocols.frag_picker.quota pyrosetta.rosetta.protocols.frag_picker.scores pyrosetta.rosetta.protocols.frags pyrosetta.rosetta.protocols.generalized_kinematic_closure pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector pyrosetta.rosetta.protocols.genetic_algorithm pyrosetta.rosetta.protocols.geometry pyrosetta.rosetta.protocols.glycan_docking pyrosetta.rosetta.protocols.glycopeptide_docking pyrosetta.rosetta.protocols.grafting pyrosetta.rosetta.protocols.grafting.simple_movers pyrosetta.rosetta.protocols.hbnet pyrosetta.rosetta.protocols.helical_bundle pyrosetta.rosetta.protocols.helical_bundle.parameters pyrosetta.rosetta.protocols.helical_bundle_predict pyrosetta.rosetta.protocols.helix_capper pyrosetta.rosetta.protocols.hotspot_hashing pyrosetta.rosetta.protocols.hotspot_hashing.movers pyrosetta.rosetta.protocols.hybridization pyrosetta.rosetta.protocols.hydrate pyrosetta.rosetta.protocols.idealize pyrosetta.rosetta.protocols.indel pyrosetta.rosetta.protocols.indexed_structure_store pyrosetta.rosetta.protocols.indexed_structure_store.filters pyrosetta.rosetta.protocols.indexed_structure_store.movers pyrosetta.rosetta.protocols.indexed_structure_store.search pyrosetta.rosetta.protocols.init pyrosetta.rosetta.protocols.interface pyrosetta.rosetta.protocols.jd2 pyrosetta.rosetta.protocols.jd2.archive pyrosetta.rosetta.protocols.jd2.JobInputterInputSource pyrosetta.rosetta.protocols.jd3 pyrosetta.rosetta.protocols.jd3.chunk_library pyrosetta.rosetta.protocols.jd3.chunk_library_inputters pyrosetta.rosetta.protocols.jd3.dag_node_managers pyrosetta.rosetta.protocols.jd3.deallocation pyrosetta.rosetta.protocols.jd3.full_model pyrosetta.rosetta.protocols.jd3.full_model_inputters pyrosetta.rosetta.protocols.jd3.job_distributors pyrosetta.rosetta.protocols.jd3.job_results pyrosetta.rosetta.protocols.jd3.job_summaries pyrosetta.rosetta.protocols.jd3.jobs pyrosetta.rosetta.protocols.jd3.output pyrosetta.rosetta.protocols.jd3.pose_inputters pyrosetta.rosetta.protocols.jd3.pose_outputters pyrosetta.rosetta.protocols.jd3.standard pyrosetta.rosetta.protocols.jobdist pyrosetta.rosetta.protocols.jumping pyrosetta.rosetta.protocols.kinematic_closure pyrosetta.rosetta.protocols.kinematic_closure.perturbers pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers pyrosetta.rosetta.protocols.kinmatch pyrosetta.rosetta.protocols.legacy_sewing pyrosetta.rosetta.protocols.legacy_sewing.sampling pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements pyrosetta.rosetta.protocols.legacy_sewing.scoring pyrosetta.rosetta.protocols.ligand_docking pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock pyrosetta.rosetta.protocols.ligand_docking.ligand_options pyrosetta.rosetta.protocols.ligand_docking.rdf pyrosetta.rosetta.protocols.loop_build pyrosetta.rosetta.protocols.loop_grower pyrosetta.rosetta.protocols.loop_modeler pyrosetta.rosetta.protocols.loop_modeler.perturbers pyrosetta.rosetta.protocols.loop_modeling pyrosetta.rosetta.protocols.loop_modeling.refiners pyrosetta.rosetta.protocols.loop_modeling.samplers pyrosetta.rosetta.protocols.loop_modeling.utilities pyrosetta.rosetta.protocols.loophash pyrosetta.rosetta.protocols.loops pyrosetta.rosetta.protocols.loops.filters pyrosetta.rosetta.protocols.loops.loop_closure pyrosetta.rosetta.protocols.loops.loop_closure.ccd pyrosetta.rosetta.protocols.loops.loop_closure.jacobi pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure pyrosetta.rosetta.protocols.loops.loop_mover pyrosetta.rosetta.protocols.loops.loop_mover.perturb pyrosetta.rosetta.protocols.loops.loop_mover.refine pyrosetta.rosetta.protocols.loops.loops_definers pyrosetta.rosetta.protocols.magnesium pyrosetta.rosetta.protocols.mainchain_potential pyrosetta.rosetta.protocols.make_rot_lib pyrosetta.rosetta.protocols.match pyrosetta.rosetta.protocols.match.downstream pyrosetta.rosetta.protocols.match.output pyrosetta.rosetta.protocols.match.upstream pyrosetta.rosetta.protocols.matdes pyrosetta.rosetta.protocols.md pyrosetta.rosetta.protocols.mean_field pyrosetta.rosetta.protocols.medal pyrosetta.rosetta.protocols.membrane pyrosetta.rosetta.protocols.membrane.benchmark pyrosetta.rosetta.protocols.membrane.geometry pyrosetta.rosetta.protocols.membrane.scoring pyrosetta.rosetta.protocols.membrane.symmetry pyrosetta.rosetta.protocols.membrane.visualize pyrosetta.rosetta.protocols.membrane_benchmark pyrosetta.rosetta.protocols.metal_interface pyrosetta.rosetta.protocols.minimization_packing pyrosetta.rosetta.protocols.minimization_packing.symmetry pyrosetta.rosetta.protocols.monte_carlo pyrosetta.rosetta.protocols.motif_grafting pyrosetta.rosetta.protocols.motif_grafting.movers pyrosetta.rosetta.protocols.motifs pyrosetta.rosetta.protocols.moves pyrosetta.rosetta.protocols.mpi_refinement pyrosetta.rosetta.protocols.multistage_rosetta_scripts pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics pyrosetta.rosetta.protocols.multistate_design pyrosetta.rosetta.protocols.ncbb pyrosetta.rosetta.protocols.ncbb.oop pyrosetta.rosetta.protocols.neighbor pyrosetta.rosetta.protocols.network pyrosetta.rosetta.protocols.nmr pyrosetta.rosetta.protocols.nmr.pcs pyrosetta.rosetta.protocols.nmr.pre pyrosetta.rosetta.protocols.nmr.rdc pyrosetta.rosetta.protocols.noesy_assign pyrosetta.rosetta.protocols.normalmode pyrosetta.rosetta.protocols.optimize_weights pyrosetta.rosetta.protocols.pack_daemon pyrosetta.rosetta.protocols.pack_interface pyrosetta.rosetta.protocols.parser pyrosetta.rosetta.protocols.pb_potential pyrosetta.rosetta.protocols.pdbinfo_manipulations pyrosetta.rosetta.protocols.peptide_deriver pyrosetta.rosetta.protocols.pmut_scan pyrosetta.rosetta.protocols.pockets pyrosetta.rosetta.protocols.pose_creation pyrosetta.rosetta.protocols.pose_length_moves pyrosetta.rosetta.protocols.pose_metric_calculators pyrosetta.rosetta.protocols.pose_reporters pyrosetta.rosetta.protocols.pose_selectors pyrosetta.rosetta.protocols.pose_sewing pyrosetta.rosetta.protocols.pose_sewing.data_storage pyrosetta.rosetta.protocols.pose_sewing.filters pyrosetta.rosetta.protocols.pose_sewing.movers pyrosetta.rosetta.protocols.pose_sewing.simple_metrics pyrosetta.rosetta.protocols.protein_interface_design pyrosetta.rosetta.protocols.protein_interface_design.filters pyrosetta.rosetta.protocols.protein_interface_design.movers pyrosetta.rosetta.protocols.protein_mpnn pyrosetta.rosetta.protocols.ptm_prediction pyrosetta.rosetta.protocols.qsar pyrosetta.rosetta.protocols.qsar.scoring_grid pyrosetta.rosetta.protocols.quantum_annealing pyrosetta.rosetta.protocols.rbsegment_relax pyrosetta.rosetta.protocols.recces pyrosetta.rosetta.protocols.recces.options pyrosetta.rosetta.protocols.recces.params pyrosetta.rosetta.protocols.recces.sampler pyrosetta.rosetta.protocols.recces.sampler.rna pyrosetta.rosetta.protocols.recces.scratch pyrosetta.rosetta.protocols.recon_design pyrosetta.rosetta.protocols.relax pyrosetta.rosetta.protocols.relax.loop pyrosetta.rosetta.protocols.relax.membrane pyrosetta.rosetta.protocols.residue_optimization pyrosetta.rosetta.protocols.residue_selectors pyrosetta.rosetta.protocols.rigid pyrosetta.rosetta.protocols.rna pyrosetta.rosetta.protocols.rna.denovo pyrosetta.rosetta.protocols.rna.denovo.coarse pyrosetta.rosetta.protocols.rna.denovo.movers pyrosetta.rosetta.protocols.rna.denovo.output pyrosetta.rosetta.protocols.rna.movers pyrosetta.rosetta.protocols.rna.setup pyrosetta.rosetta.protocols.rosetta_scripts pyrosetta.rosetta.protocols.rotamer_recovery pyrosetta.rosetta.protocols.RotamerDump pyrosetta.rosetta.protocols.rpc pyrosetta.rosetta.protocols.sasa_scores pyrosetta.rosetta.protocols.score_filters pyrosetta.rosetta.protocols.scoring pyrosetta.rosetta.protocols.scoring.methods pyrosetta.rosetta.protocols.scoring.methods.pcs pyrosetta.rosetta.protocols.scoring.methods.pcs2 pyrosetta.rosetta.protocols.scoring.methods.pcsTs1 pyrosetta.rosetta.protocols.scoring.methods.pcsTs2 pyrosetta.rosetta.protocols.scoring.methods.pcsTs3 pyrosetta.rosetta.protocols.scoring.methods.pcsTs4 pyrosetta.rosetta.protocols.scoring.methods.saxs pyrosetta.rosetta.protocols.seeded_abinitio pyrosetta.rosetta.protocols.sewing pyrosetta.rosetta.protocols.sewing.data_storage pyrosetta.rosetta.protocols.sewing.hashing pyrosetta.rosetta.protocols.sewing.movers pyrosetta.rosetta.protocols.sewing.requirements pyrosetta.rosetta.protocols.sewing.scoring pyrosetta.rosetta.protocols.sic_dock pyrosetta.rosetta.protocols.sic_dock.scores pyrosetta.rosetta.protocols.simple_ddg pyrosetta.rosetta.protocols.simple_filters pyrosetta.rosetta.protocols.simple_moves pyrosetta.rosetta.protocols.simple_moves.a3b_hbs pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock pyrosetta.rosetta.protocols.simple_moves.bb_sampler pyrosetta.rosetta.protocols.simple_moves.bin_transitions pyrosetta.rosetta.protocols.simple_moves.chiral pyrosetta.rosetta.protocols.simple_moves.hbs pyrosetta.rosetta.protocols.simple_moves.oop pyrosetta.rosetta.protocols.simple_moves.rational_mc pyrosetta.rosetta.protocols.simple_moves.sidechain_moves pyrosetta.rosetta.protocols.simple_moves.triazolamer pyrosetta.rosetta.protocols.simple_pose_metric_calculators pyrosetta.rosetta.protocols.simple_task_operations pyrosetta.rosetta.protocols.sparta pyrosetta.rosetta.protocols.splice pyrosetta.rosetta.protocols.ss_prediction pyrosetta.rosetta.protocols.star pyrosetta.rosetta.protocols.stepwise pyrosetta.rosetta.protocols.stepwise.legacy pyrosetta.rosetta.protocols.stepwise.legacy.modeler pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna pyrosetta.rosetta.protocols.stepwise.legacy.screener pyrosetta.rosetta.protocols.stepwise.modeler pyrosetta.rosetta.protocols.stepwise.modeler.align pyrosetta.rosetta.protocols.stepwise.modeler.movemap pyrosetta.rosetta.protocols.stepwise.modeler.options pyrosetta.rosetta.protocols.stepwise.modeler.packer pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens pyrosetta.rosetta.protocols.stepwise.modeler.precomputed pyrosetta.rosetta.protocols.stepwise.modeler.protein pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close pyrosetta.rosetta.protocols.stepwise.modeler.rna pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters pyrosetta.rosetta.protocols.stepwise.monte_carlo pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options pyrosetta.rosetta.protocols.stepwise.monte_carlo.options pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna pyrosetta.rosetta.protocols.stepwise.monte_carlo.submotif pyrosetta.rosetta.protocols.stepwise.options pyrosetta.rosetta.protocols.stepwise.sampler pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs pyrosetta.rosetta.protocols.stepwise.sampler.input_streams pyrosetta.rosetta.protocols.stepwise.sampler.jump pyrosetta.rosetta.protocols.stepwise.sampler.protein pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body pyrosetta.rosetta.protocols.stepwise.sampler.rna pyrosetta.rosetta.protocols.stepwise.sampler.screener pyrosetta.rosetta.protocols.stepwise.screener pyrosetta.rosetta.protocols.stepwise.setup pyrosetta.rosetta.protocols.struct_fragment pyrosetta.rosetta.protocols.surface_docking pyrosetta.rosetta.protocols.switches pyrosetta.rosetta.protocols.symmetric_docking pyrosetta.rosetta.protocols.symmetric_docking.membrane pyrosetta.rosetta.protocols.symmetry pyrosetta.rosetta.protocols.task_operations pyrosetta.rosetta.protocols.tcr pyrosetta.rosetta.protocols.testing pyrosetta.rosetta.protocols.toolbox pyrosetta.rosetta.protocols.toolbox.match_enzdes_util pyrosetta.rosetta.protocols.toolbox.pose_manipulation pyrosetta.rosetta.protocols.toolbox.py_inheritance_test pyrosetta.rosetta.protocols.toolbox.rigid_body pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations pyrosetta.rosetta.protocols.toolbox.sample_around pyrosetta.rosetta.protocols.topology_broker pyrosetta.rosetta.protocols.topology_broker.claims pyrosetta.rosetta.protocols.topology_broker.weights pyrosetta.rosetta.protocols.trajectory pyrosetta.rosetta.protocols.trRosetta pyrosetta.rosetta.protocols.trRosetta_protocols pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators pyrosetta.rosetta.protocols.trRosetta_protocols.movers pyrosetta.rosetta.protocols.ub_e2c pyrosetta.rosetta.protocols.unfolded_state_energy_calculator pyrosetta.rosetta.protocols.vardist_solaccess pyrosetta.rosetta.protocols.viewer pyrosetta.rosetta.protocols.viewer.graphics_states_param pyrosetta.rosetta.protocols.vip pyrosetta.rosetta.protocols.wum pyrosetta.rosetta.RDGeom pyrosetta.rosetta.RDKit pyrosetta.rosetta.std pyrosetta.rosetta.utility pyrosetta.rosetta.utility.CSI pyrosetta.rosetta.utility.excn pyrosetta.rosetta.utility.factory pyrosetta.rosetta.utility.file pyrosetta.rosetta.utility.graph pyrosetta.rosetta.utility.io pyrosetta.rosetta.utility.io.mpi_stream pyrosetta.rosetta.utility.json_spirit pyrosetta.rosetta.utility.json_spirit.internal_ pyrosetta.rosetta.utility.keys pyrosetta.rosetta.utility.libsvm pyrosetta.rosetta.utility.options pyrosetta.rosetta.utility.pointer pyrosetta.rosetta.utility.py pyrosetta.rosetta.utility.signals pyrosetta.rosetta.utility.sql_database pyrosetta.rosetta.utility.tag pyrosetta.rosetta.utility.thread pyrosetta.rosetta.utility.tools pyrosetta.rosetta.utility.type_traits pyrosetta.rosetta.utility.type_traits.has_insertion_operator_implementation pyrosetta.rosetta.utility.xsd_util pyrosetta.rosetta.utility_exit_detail pyrosetta.teaching pyrosetta.tests pyrosetta.tests.bindings pyrosetta.tests.bindings.core pyrosetta.tests.bindings.core.test_pose pyrosetta.tests.distributed pyrosetta.tests.distributed.cluster pyrosetta.tests.distributed.test_dask_worker pyrosetta.tests.numeric pyrosetta.tests.protocols pyrosetta.tests.protocols.indexed_structure_store pyrosetta.toolbox pyrosetta.toolbox.atom_pair_energy pyrosetta.toolbox.cleaning pyrosetta.toolbox.extract_coords_pose pyrosetta.toolbox.generate_resfile pyrosetta.toolbox.mutants pyrosetta.toolbox.numpy_utils pyrosetta.toolbox.py_jobdistributor pyrosetta.toolbox.rcsb pyrosetta.utility module_name() (pyrosetta.rosetta.basic.citation_manager.CitationCollection method) (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo method) module_type() (pyrosetta.rosetta.basic.citation_manager.CitationCollection method) (pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo method) modules_ (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians property) ModuleType1 (class in pyrosetta.rosetta.core.kinematics.jacobian) ModuleType1.jacobian_struct (class in pyrosetta.rosetta.core.kinematics.jacobian) ModuleType1.screw_construct_struct (class in pyrosetta.rosetta.core.kinematics.jacobian) modulo() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.numeric.ModuloSelector_double_false_t static method) (pyrosetta.rosetta.numeric.ModuloSelector_int_true_t static method) ModuloSelector_double_false_t (class in pyrosetta.rosetta.numeric) ModuloSelector_int_true_t (class in pyrosetta.rosetta.numeric) MOL_ID (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) MolarMassFilter (class in pyrosetta.rosetta.protocols.ligand_docking) MolarMassFilterCreator (class in pyrosetta.rosetta.protocols.ligand_docking) MolecularDynamics (class in pyrosetta.rosetta.protocols.cartesian) MolecularMassFilter (class in pyrosetta.rosetta.protocols.ligand_docking) MolecularMassFilterCreator (class in pyrosetta.rosetta.protocols.ligand_docking) MolecularSurfaceCalculator (class in pyrosetta.rosetta.core.scoring.sc) MolecularWeightNormalization (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) MOLECULE (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) molecule (pyrosetta.rosetta.core.scoring.sc.Atom property) MolFileIOAtom (class in pyrosetta.rosetta.core.chemical.sdf) MolFileIOBond (class in pyrosetta.rosetta.core.chemical.sdf) MolFileIOMolecule (class in pyrosetta.rosetta.core.chemical.sdf) MolFileIOReader (class in pyrosetta.rosetta.core.chemical.sdf) moltenres() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) moltenres_2_resid() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) moltenres_2_resid_vector() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) moltenres_atomtree_collection() (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) moltenres_for_rotamer() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) moltenres_for_sample_rot() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) moltenres_part_of_flexsegment() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) moltenres_rotid_2_rotid() (pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) (pyrosetta.rosetta.core.pack_basic.RotamerSetsBase method) (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) moltenresid (pyrosetta.rosetta.core.pack.annealer.RotSub property) moltenresid_2_resid() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) MolWriter (class in pyrosetta.rosetta.core.chemical.sdf) momento_for_moltenres() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) MONOCLINIC (pyrosetta.rosetta.protocols.cryst.SpacegroupSetting attribute) monopole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) (pyrosetta.rosetta.core.scoring.MultipoleParameter method) monte_carlo() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) monte_carlo_cycles() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) monte_carlo_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.MonteCarloLoader static method) monte_carlo_seed() (pyrosetta.rosetta.protocols.hbnet.NetworkState method) MonteCarlo (class in pyrosetta.rosetta.protocols.moves) MonteCarloExceptionConverge (class in pyrosetta.rosetta.protocols.moves) MonteCarloInterface (class in pyrosetta.rosetta.protocols.monte_carlo) MonteCarloLoader (class in pyrosetta.rosetta.protocols.parser) MonteCarloLoaderCreator (class in pyrosetta.rosetta.protocols.parser) MonteCarloRecover (class in pyrosetta.rosetta.protocols.monte_carlo) MonteCarloRecoverCreator (class in pyrosetta.rosetta.protocols.monte_carlo) MonteCarloReset (class in pyrosetta.rosetta.protocols.monte_carlo) MonteCarloResetCreator (class in pyrosetta.rosetta.protocols.monte_carlo) MonteCarloTest (class in pyrosetta.rosetta.protocols.monte_carlo) MonteCarloTestCreator (class in pyrosetta.rosetta.protocols.monte_carlo) MonteCarloUtil (class in pyrosetta.rosetta.protocols.moves) more_ancient_ptr (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct property) (pyrosetta.rosetta.utility.history_queue_struct property) more_precise_base_pair_classification() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) more_recent_ptr (pyrosetta.rosetta.core.pack.interaction_graph.history_queue_struct property) (pyrosetta.rosetta.utility.history_queue_struct property) morpheme_from_ring_size() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) MOST_FREQ_BASED (pyrosetta.rosetta.protocols.cluster.calibur.EST_THRESHOLD_MODE attribute) most_probable_bin() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) Motif (class in pyrosetta.rosetta.protocols.motifs) motif (pyrosetta.rosetta.core.scoring.motif.MotifHit property) motif2scaffold_data (class in pyrosetta.rosetta.protocols.motif_grafting.movers) motif2scaffold_indexes (class in pyrosetta.rosetta.protocols.motif_grafting.movers) motif_bin_hash() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner method) motif_bin_label() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifMetaBinner method) motif_dock (pyrosetta.rosetta.core.scoring.ScoreType attribute) motif_fragments_RMSD (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_data property) motif_hash() (pyrosetta.rosetta.protocols.sic_dock.scores.MotifHashRigidScore method) motif_label() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) motif_library() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) motif_set_names() (pyrosetta.rosetta.core.scoring.motif.MotifHashManager method) motif_umap_ (pyrosetta.rosetta.core.scoring.motif.MotifHash property) MotifArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) MotifArchitectCreator (class in pyrosetta.rosetta.protocols.denovo_design.architects) motifcop() (pyrosetta.rosetta.protocols.motifs.MotifHit method) MotifDnaPacker (class in pyrosetta.rosetta.protocols.motifs) MotifDnaPackerCreator (class in pyrosetta.rosetta.protocols.motifs) MotifDockEnergy (class in pyrosetta.rosetta.core.energy_methods) MotifDockEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MotifGraftCreator (class in pyrosetta.rosetta.protocols.motif_grafting.movers) MotifGraftMover (class in pyrosetta.rosetta.protocols.motif_grafting.movers) MotifHash (class in pyrosetta.rosetta.core.scoring.motif) MotifHashManager (class in pyrosetta.rosetta.core.scoring.motif) MotifHashRigidScore (class in pyrosetta.rosetta.protocols.sic_dock.scores) motifHigh (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes property) MotifHit (class in pyrosetta.rosetta.core.scoring.motif) (class in pyrosetta.rosetta.protocols.motifs) MotifHits (class in pyrosetta.rosetta.core.scoring.motif) MotifHitsRotamersOperation (class in pyrosetta.rosetta.protocols.matdes) MotifHitStats (class in pyrosetta.rosetta.core.scoring.motif) MotifLibrary (class in pyrosetta.rosetta.protocols.motifs) motifLow (pyrosetta.rosetta.protocols.motif_grafting.movers.motif2scaffold_indexes property) MotifMatch (class in pyrosetta.rosetta.protocols.motif_grafting.movers) MotifMatchOverlapReq (class in pyrosetta.rosetta.core.scoring.motif) motifs() (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect method) MotifScoreFilter (class in pyrosetta.rosetta.protocols.simple_filters) MotifScoreFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) MotifScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) MotifScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) MotifSearch (class in pyrosetta.rosetta.protocols.motifs) movable_chains() (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) movable_group() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) movable_groups() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) movable_jumps() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.RigidBodyInfo method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) move() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) move_all_inserted() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) move_apart() (in module pyrosetta.rosetta.protocols.docking) move_apart_first() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) move_atoms_to_collcheck_begin() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) move_away() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) move_back() (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) move_distance (pyrosetta.rosetta.protocols.ligand_docking.Transform_info property) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info property) move_element() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) move_first_rigid_body() (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) move_jump_points_away() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.TransientCutpointHandler method) move_jumps_between_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) move_ligand_and_update_rhos_() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) move_ligand_neighbor_to_desired_position() (in module pyrosetta.rosetta.protocols.ligand_docking) move_ligand_to_desired_centroid() (in module pyrosetta.rosetta.protocols.ligand_docking) move_map() (pyrosetta.rosetta.core.kinematics.jacobian.SeriesJacobians method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) move_map_action (class in pyrosetta.rosetta.core.select.movemap) move_map_from_loop() (in module pyrosetta.rosetta.protocols.loops) move_map_from_loops() (in module pyrosetta.rosetta.protocols.loops) move_pose_to_standard_orie() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) move_segment() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) move_together() (in module pyrosetta.rosetta.protocols.docking) move_type (class in pyrosetta.rosetta.protocols.legacy_sewing) move_type() (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) move_type_from_string() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) move_type_string() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) move_with_rama() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) move_with_scorefxn() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) moveable_jump() (in module pyrosetta.rosetta.core.pose.rna) MoveBeforeFilter (class in pyrosetta.rosetta.protocols.filters) MoveBeforeFilterCreator (class in pyrosetta.rosetta.protocols.filters) moved() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.scoring.EnergyNode method) moveFromStubFrame() (pyrosetta.rosetta.protocols.hotspot_hashing.StubGenerator static method) moveIntoStubFrame() (pyrosetta.rosetta.protocols.hotspot_hashing.StubGenerator static method) MoveMap (class in pyrosetta.rosetta.core.kinematics) movemap() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) (pyrosetta.rosetta.protocols.forge.build.Bridge method) (pyrosetta.rosetta.protocols.forge.build.BuildInstruction method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) (pyrosetta.rosetta.protocols.forge.build.SegmentRebuild method) (pyrosetta.rosetta.protocols.forge.build.SegmentSwap method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.LoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ShortLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) movemap_as_OP() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) movemap_builder_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader static method) movemap_cen() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_cen_all() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_cen_omegafixed() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_disables_packing_of_fixed_chi_positions() (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.relax.FastRelax method) movemap_fa() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_fa_all() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_fa_omegafixed() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) movemap_factory() (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) movemap_factory_category() (in module pyrosetta.rosetta.core.select.movemap) movemap_from_blueprint() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) movemap_from_pose() (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) movemap_ptr() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) movemap_setup() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) MoveMapBuilder (class in pyrosetta.rosetta.protocols.ligand_docking) MoveMapBuilderLoader (class in pyrosetta.rosetta.protocols.ligand_docking) MoveMapBuilderLoaderCreator (class in pyrosetta.rosetta.protocols.ligand_docking) MoveMapFactory (class in pyrosetta.rosetta.core.select.movemap) movemapfactory() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) MoveMapFactoryLoader (class in pyrosetta.rosetta.protocols.parser) MoveMapFactoryLoaderCreator (class in pyrosetta.rosetta.protocols.parser) MoveMapFactoryToNamedMoveMapMover (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) MoveMapFactoryToNamedMoveMapMoverCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.movers) MoveMapMover (class in pyrosetta.rosetta.protocols.moves) MovePoseToMembraneCenterMover (class in pyrosetta.rosetta.protocols.rigid) Mover (class in pyrosetta.rosetta.protocols.moves) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) mover (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter property) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep property) mover() (pyrosetta.rosetta.core.environment.DofPassport method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.jd3.chunk_library.MoverAndChunkLibraryJob method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) mover_creator_map() (pyrosetta.rosetta.protocols.moves.MoverFactory method) mover_exists() (pyrosetta.rosetta.protocols.moves.MoverFactory method) Mover_LoopHashRefine (class in pyrosetta.rosetta.protocols.loophash) mover_mode() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) mover_name() (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover static method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer static method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM static method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly static method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover static method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover static method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover static method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter static method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover static method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator static method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock static method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover static method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro static method) (pyrosetta.rosetta.protocols.backrub.BackrubMover static method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol static method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator static method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange static method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator static method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator static method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver static method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler static method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens static method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover static method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover static method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover static method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover static method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover static method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints static method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints static method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover static method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover static method) (pyrosetta.rosetta.protocols.contact_map.ContactMap static method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol static method) (pyrosetta.rosetta.protocols.cryst.CrystRMS static method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover static method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover static method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover static method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover static method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover static method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover static method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover static method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover static method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover static method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover static method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo static method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover static method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign static method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations static method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover static method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover static method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign static method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker static method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna static method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover static method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy static method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation static method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact static method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol static method) (pyrosetta.rosetta.protocols.docking.DockMinMover static method) (pyrosetta.rosetta.protocols.docking.DockSetupMover static method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator static method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator static method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol static method) (pyrosetta.rosetta.protocols.docking.TemperedDockingCreator static method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover static method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover static method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover static method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores static method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC static method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities static method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover static method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover static method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM static method) (pyrosetta.rosetta.protocols.environment.EnvMover static method) (pyrosetta.rosetta.protocols.environment.ScriptCM static method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts static method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler static method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize static method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy static method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover static method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover static method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover static method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation static method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover static method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover static method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover static method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator static method) (pyrosetta.rosetta.protocols.features.ReportToDB static method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB static method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR static method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation static method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover static method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential static method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies static method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol static method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign static method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack static method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover static method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover static method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG static method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC static method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol static method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover static method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover static method) (pyrosetta.rosetta.protocols.hbnet.HBNet static method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface static method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler static method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler static method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle static method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle static method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix static method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe static method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation static method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler static method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler static method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol static method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover static method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover static method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover static method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover static method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover static method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens static method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate static method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF static method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer static method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock static method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand static method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker static method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign static method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone static method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers static method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate static method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates static method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether static method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom static method) (pyrosetta.rosetta.protocols.ligand_docking.Transform static method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.Translate static method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile static method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper static method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow static method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension static method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom static method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier static method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper static method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover static method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover static method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial static method) (pyrosetta.rosetta.protocols.match.MatcherMover static method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover static method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover static method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover static method) (pyrosetta.rosetta.protocols.matdes.SymDofMover static method) (pyrosetta.rosetta.protocols.md.CartesianMD static method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint static method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover static method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder static method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix static method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles static method) (pyrosetta.rosetta.protocols.membrane.FlipMover static method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator static method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover static method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility static method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover static method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator static method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover static method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover static method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler static method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover static method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover static method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover static method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator static method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator static method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest static method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover static method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover static method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker static method) (pyrosetta.rosetta.protocols.moves.DsspMover static method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover static method) (pyrosetta.rosetta.protocols.moves.IfMover static method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover static method) (pyrosetta.rosetta.protocols.moves.PyMOLMover static method) (pyrosetta.rosetta.protocols.moves.RampingMover static method) (pyrosetta.rosetta.protocols.moves.RandomMover static method) (pyrosetta.rosetta.protocols.moves.SequenceMover static method) (pyrosetta.rosetta.protocols.moves.SwitchMover static method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol static method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover static method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol static method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover static method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinderCreator static method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover static method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover static method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover static method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover static method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer static method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover static method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential static method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences static method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover static method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover static method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover static method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover static method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover static method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover static method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling static method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChangeCreator static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover static method) (pyrosetta.rosetta.protocols.qsar.qsarCreator static method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage static method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader static method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover static method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer static method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover static method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator static method) (pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator static method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover static method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMoverCreator static method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover static method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMoverCreator static method) (pyrosetta.rosetta.protocols.relax.ClassicRelaxCreator static method) (pyrosetta.rosetta.protocols.relax.FastRelax static method) (pyrosetta.rosetta.protocols.relax.LocalRelax static method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover static method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover static method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax static method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover static method) (pyrosetta.rosetta.protocols.rigid.RollMover static method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM static method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover static method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol static method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol static method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify static method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover static method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapperCreator static method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper static method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover static method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol static method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover static method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst static method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops static method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment static method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMoverCreator static method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMoverCreator static method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMoverCreator static method) (pyrosetta.rosetta.protocols.simple_ddg.ddG static method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData static method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint static method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator static method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover static method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover static method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator static method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover static method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins static method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins static method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover static method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover static method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover static method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover static method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator static method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond static method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover static method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover static method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb static method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers static method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover static method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator static method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile static method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence static method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif static method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover static method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover static method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology static method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover static method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue static method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover static method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover static method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover static method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover static method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover static method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover static method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover static method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA static method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ static method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree static method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover static method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover static method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities static method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover static method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover static method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover static method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover static method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion static method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover static method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator static method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover static method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover static method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot static method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover static method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover static method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover static method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover static method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover static method) (pyrosetta.rosetta.protocols.simple_moves.Tumble static method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover static method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose static method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover static method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover static method) (pyrosetta.rosetta.protocols.splice.RBInMover static method) (pyrosetta.rosetta.protocols.splice.RBOutMover static method) (pyrosetta.rosetta.protocols.splice.RotLibOut static method) (pyrosetta.rosetta.protocols.splice.RotLibOutCreator static method) (pyrosetta.rosetta.protocols.splice.Splice static method) (pyrosetta.rosetta.protocols.splice.SpliceCreator static method) (pyrosetta.rosetta.protocols.splice.SpliceIn static method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody static method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator static method) (pyrosetta.rosetta.protocols.splice.SpliceInCreator static method) (pyrosetta.rosetta.protocols.splice.SpliceInTail static method) (pyrosetta.rosetta.protocols.splice.SpliceInTailCreator static method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.splice.SpliceOut static method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody static method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibodyCreator static method) (pyrosetta.rosetta.protocols.splice.SpliceOutCreator static method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail static method) (pyrosetta.rosetta.protocols.splice.SpliceOutTailCreator static method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover static method) (pyrosetta.rosetta.protocols.splice.TailSegmentMoverCreator static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover static method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover static method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover static method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry static method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover static method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover static method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover static method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMoverCreator static method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover static method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover static method) mover_or_add_group_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover static method) mover_or_filter (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) mover_stopping_condition() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) mover_tag() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) mover_tags (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.ParsedTagCache property) mover_user_name (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep property) mover_weight() (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) mover_xml_schema_group_name() (pyrosetta.rosetta.protocols.moves.MoverFactory static method) MoverAndChunkLibraryJob (class in pyrosetta.rosetta.protocols.jd3.chunk_library) MoverApplyingMover (class in pyrosetta.rosetta.protocols.moves) MoverContainer (class in pyrosetta.rosetta.protocols.moves) MoverCreator (class in pyrosetta.rosetta.protocols.moves) MoverFactory (class in pyrosetta.rosetta.protocols.moves) MoverForPoseList (class in pyrosetta.rosetta.protocols.moves) MoverJob (class in pyrosetta.rosetta.protocols.jd3.jobs) moverkey() (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.JumpSampleData method) MoverList (class in pyrosetta.rosetta.protocols.wum) movers() (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) MoverStatistics (class in pyrosetta.rosetta.protocols.moves) MoverStatus (class in pyrosetta.rosetta.protocols.moves) movertype (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) moves_residue() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) MoveType (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) moving_partition_res() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) moving_res (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) moving_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) moving_res_base_state (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) moving_res_pucker_state (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) moving_residue_at_origin() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) moving_scs() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) MP_GEOMETRY_TRANSITION (class in pyrosetta.rosetta.core.conformation.membrane) mp_param() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) mp_res_data (pyrosetta.rosetta.core.scoring.min_single_data attribute) mp_respair_data (pyrosetta.rosetta.core.scoring.min_pair_data attribute) mp_span_ang (pyrosetta.rosetta.core.scoring.ScoreType attribute) Mpair (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPCbeta (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPCbetaEnergy (class in pyrosetta.rosetta.core.energy_methods) MPCbetaEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) mPDB (pyrosetta.rosetta.protocols.cluster.calibur.Stru property) MPDockingMover (class in pyrosetta.rosetta.protocols.docking.membrane) MPDockingMoverCreator (class in pyrosetta.rosetta.protocols.docking.membrane) MPDockingSetupMover (class in pyrosetta.rosetta.protocols.docking.membrane) MPDockingSetupMoverCreator (class in pyrosetta.rosetta.protocols.docking.membrane) MPEnv (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPEnvEnergy (class in pyrosetta.rosetta.core.energy_methods) MPEnvEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MPFastRelaxMover (class in pyrosetta.rosetta.protocols.relax.membrane) MPFastRelaxMoverCreator (class in pyrosetta.rosetta.protocols.relax.membrane) MPFindInterfaceMover (class in pyrosetta.rosetta.protocols.docking.membrane) MPFindInterfaceMoverCreator (class in pyrosetta.rosetta.protocols.docking.membrane) mphbond() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) MPHelicality (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPHelicalityEnergy (class in pyrosetta.rosetta.core.energy_methods) MPHelicalityEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) mpi_bcast_seed_from_node0() (pyrosetta.rosetta.basic.random.RandomGeneratorSettings method) MPI_FAIL (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) MPI_FILE_BUF (pyrosetta.rosetta.basic.ProfTag attribute) MPI_FILE_STATUS (class in pyrosetta.rosetta.utility.io.mpi_stream) mpi_finalize() (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) MPI_GATHER_BARRIER (pyrosetta.rosetta.basic.ProfTag attribute) MPI_JD2_WAITS_FOR_ARCHIVE (pyrosetta.rosetta.basic.ProfTag attribute) MPI_LoopHashRefine (class in pyrosetta.rosetta.protocols.loophash) MPI_LoopHashRefine_Emperor (class in pyrosetta.rosetta.protocols.loophash) MPI_LoopHashRefine_Master (class in pyrosetta.rosetta.protocols.loophash) MPI_MASTER_BCAST_COORDS (pyrosetta.rosetta.basic.ProfTag attribute) MPI_MASTER_BCAST_NEW_COMM_SIZE (pyrosetta.rosetta.basic.ProfTag attribute) MPI_MASTER_BCAST_NEW_POOL_RANKS (pyrosetta.rosetta.basic.ProfTag attribute) MPI_MASTER_BCAST_NUM_STRUCTURES_TO_ADD (pyrosetta.rosetta.basic.ProfTag attribute) MPI_MASTER_BCAST_WINNING_RANKS (pyrosetta.rosetta.basic.ProfTag attribute) MPI_MASTER_BCAST_WINNING_STRUCTURES (pyrosetta.rosetta.basic.ProfTag attribute) MPI_NOTIFY_ARCHIVE (pyrosetta.rosetta.basic.ProfTag attribute) mpi_npes() (in module pyrosetta.rosetta.protocols.wum) mpi_nprocs() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) (pyrosetta.rosetta.utility.SimulateMPIData method) MPI_POOL_MASTER_THINKS (pyrosetta.rosetta.basic.ProfTag attribute) MPI_POOL_SLAVE_THINKS (pyrosetta.rosetta.basic.ProfTag attribute) mpi_rank() (in module pyrosetta.rosetta.protocols.wum) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI static method) MPI_ranks_handling_message() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary 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) MPI_Refine_Emperor (class in pyrosetta.rosetta.protocols.mpi_refinement) MPI_Refine_Master (class in pyrosetta.rosetta.protocols.mpi_refinement) MPI_Refinement (class in pyrosetta.rosetta.protocols.mpi_refinement) MPI_reroute_rank() (pyrosetta.rosetta.utility.io.ozstream static method) mpi_safe_std_err() (in module pyrosetta.rosetta.utility.options) MPI_SEND_ACCEPTED (pyrosetta.rosetta.basic.ProfTag attribute) MPI_SEND_UPDATE (pyrosetta.rosetta.basic.ProfTag attribute) MPI_SLAVE_REPORT_NEW_COORDS (pyrosetta.rosetta.basic.ProfTag attribute) MPI_SLAVE_REPORT_SIZES (pyrosetta.rosetta.basic.ProfTag attribute) MPI_STREAM_CLOSE (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) MPI_STREAM_FILE_EXIST (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) MPI_STREAM_FLUSH (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) MPI_STREAM_MSG (class in pyrosetta.rosetta.utility.io.mpi_stream) MPI_STREAM_OPEN (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) MPI_STREAM_OPEN_APPEND (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) MPI_STREAM_SEND (pyrosetta.rosetta.utility.io.mpi_stream.MPI_STREAM_MSG attribute) MPI_SUCCESS_APPEND (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) MPI_SUCCESS_NEW (pyrosetta.rosetta.utility.io.mpi_stream.MPI_FILE_STATUS attribute) MPI_SYNC_POOL_DIFF (pyrosetta.rosetta.basic.ProfTag attribute) mpi_tags (class in pyrosetta.rosetta.basic.mpi) MPI_WorkUnitManager (class in pyrosetta.rosetta.protocols.wum) MPI_WorkUnitManager_Slave (class in pyrosetta.rosetta.protocols.wum) MPIArchiveJobDistributor (class in pyrosetta.rosetta.protocols.jd2.archive) MPIArchiveJobDistributor.CompletionMessage (class in pyrosetta.rosetta.protocols.jd2.archive) MPIBARRIER (pyrosetta.rosetta.basic.ProfTag attribute) MPIBARRIER_BEGIN (pyrosetta.rosetta.basic.ProfTag attribute) MPIBARRIER_END (pyrosetta.rosetta.basic.ProfTag attribute) MPICANONICALSAMPLING (pyrosetta.rosetta.basic.ProfTag attribute) MPICOMMCREATION (pyrosetta.rosetta.basic.ProfTag attribute) MpiFileBuffer (class in pyrosetta.rosetta.protocols.jd2) MPIFileBufJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPIH_ADD_FIRST_STRUCTURE (pyrosetta.rosetta.basic.ProfTag attribute) MPIH_EVAL_AGAINST_NBR (pyrosetta.rosetta.basic.ProfTag attribute) MPIH_EVAL_CHECK_PROGRESS (pyrosetta.rosetta.basic.ProfTag attribute) MPIH_EVAL_COMMUNICATE_NEW (pyrosetta.rosetta.basic.ProfTag attribute) MPIH_PREPARE_WRITE_STRUCTURES (pyrosetta.rosetta.basic.ProfTag attribute) MPIH_UPDATE_EVAL (pyrosetta.rosetta.basic.ProfTag attribute) MPIH_WRITE_STRUCT (pyrosetta.rosetta.basic.ProfTag attribute) MPIMultiCommJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPIMultistateFitnessFunction (class in pyrosetta.rosetta.protocols.pack_daemon) MPIPOOLCOMMUNICATION (pyrosetta.rosetta.basic.ProfTag attribute) MPIWorkPartitionJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPIWorkPoolJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPLipidAccessibility (class in pyrosetta.rosetta.protocols.membrane) MPLipidAccessibilityCreator (class in pyrosetta.rosetta.protocols.membrane) MPLipo (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPMutateRelaxMover (class in pyrosetta.rosetta.protocols.membrane) MPMutateRelaxMoverCreator (class in pyrosetta.rosetta.protocols.membrane) MPNonHelix (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPNonHelixPenalty (class in pyrosetta.rosetta.core.scoring.membrane) MPNonHelixPenaltyCreator (class in pyrosetta.rosetta.core.scoring.membrane) mpose() (pyrosetta.rosetta.core.scoring.motif.MotifHit method) mpose_ (pyrosetta.rosetta.core.scoring.motif.MotifHit property) mposeptr() (pyrosetta.rosetta.core.scoring.motif.MotifHit method) MPPair (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPPairEnergy (class in pyrosetta.rosetta.core.energy_methods) MPPairEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MPQuickRelaxMover (class in pyrosetta.rosetta.protocols.membrane) MPQuickRelaxMoverCreator (class in pyrosetta.rosetta.protocols.membrane) MPRangeRelaxMover (class in pyrosetta.rosetta.protocols.relax.membrane) MPResidueLipophilicity (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPResidueLipophilicityEnergy (class in pyrosetta.rosetta.core.energy_methods) MPResidueLipophilicityEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MPSpanAngleEnergy (class in pyrosetta.rosetta.core.energy_methods) MPSpanAngleEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MPSpanAngleFilter (class in pyrosetta.rosetta.protocols.simple_filters) MPSpanAngleFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) MPSpanInsertionEnergy (class in pyrosetta.rosetta.core.energy_methods) MPSpanInsertionEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MPSymDockMover (class in pyrosetta.rosetta.protocols.symmetric_docking.membrane) MPSymDockMoverCreator (class in pyrosetta.rosetta.protocols.symmetric_docking.membrane) MPTermini (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPTerminiPenalty (class in pyrosetta.rosetta.core.scoring.membrane) MPTerminiPenaltyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPTMProj (pyrosetta.rosetta.core.scoring.ScoreType attribute) MPTMProjPenalty (class in pyrosetta.rosetta.core.scoring.membrane) MPTMProjPenaltyCreator (class in pyrosetta.rosetta.core.scoring.membrane) mrb_do_not_merge (pyrosetta.rosetta.core.chemical.io.merge_residue_behavior attribute) mrb_merge_w_next (pyrosetta.rosetta.core.chemical.io.merge_residue_behavior attribute) mrb_merge_w_prev (pyrosetta.rosetta.core.chemical.io.merge_residue_behavior attribute) mRemainingSize (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) mres_has_heavy_unsats() (pyrosetta.rosetta.protocols.hbnet.NetworkState method) mres_has_unsats() (pyrosetta.rosetta.protocols.hbnet.NetworkState method) MRMover (class in pyrosetta.rosetta.protocols.hybridization) MRSJob (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) MRSJobQueen (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) MRSJobQueenChecker (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) MRSJobSummary (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) MS_FAIL (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) MS_FAIL_BAD_INPUT (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) MS_FAIL_DO_NOT_RETRY (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) MS_FAIL_RETRY (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) MS_SUCCESS (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) msa() (pyrosetta.rosetta.core.scoring.packstat.PackingScoreResData method) msas_for_atom() (pyrosetta.rosetta.protocols.vardist_solaccess.VarSolDRotamerDots method) MSDMover (class in pyrosetta.rosetta.protocols.recon_design) MSDMoverCreator (class in pyrosetta.rosetta.protocols.recon_design) msg() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.excn.Exception method) (pyrosetta.rosetta.utility.excn.FileNotFound method) (pyrosetta.rosetta.utility.excn.IOError method) (pyrosetta.rosetta.utility.excn.KeyError method) (pyrosetta.rosetta.utility.excn.NullPointerError method) (pyrosetta.rosetta.utility.excn.RangeError method) (pyrosetta.rosetta.utility.excn.RosettaScriptsOptionError method) (pyrosetta.rosetta.utility.excn.UserCorrectableIssue method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) msg_tag (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor.CompletionMessage property) msg_type() (pyrosetta.rosetta.utility.SimulateMPIMessage method) mstype_from_name() (in module pyrosetta.rosetta.protocols.moves) Mt (pyrosetta.rosetta.core.chemical.element.Elements attribute) mt19937_RG (class in pyrosetta.rosetta.numeric.random) MTRIX1 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) MTRIX2 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) MTRIX3 (pyrosetta.rosetta.core.io.pdb.RecordType attribute) mu() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters method) MU_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) MulliganPNearEvaluator (class in pyrosetta.rosetta.protocols.toolbox) multi_component() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) multi_cool_annealer() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) multi_cool_annealer_history_size() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) multi_fast_relax() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) multi_origin_list() (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) multi_rb() (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) multi_relative() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) multi_threading_inner_job() (pyrosetta.rosetta.protocols.jd2.MultiThreadingJob method) multi_use() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) multicomp() (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) MultiConstraint (class in pyrosetta.rosetta.core.scoring.constraints) MultiConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) MultiCoolAnnealer (class in pyrosetta.rosetta.core.pack.annealer) MultiDimensionalHistogram (class in pyrosetta.rosetta.numeric) Multifunc (class in pyrosetta.rosetta.core.optimization) multimap_double_std_pair_unsigned_long_std_pair_std_shared_ptr_protocols_hotspot_hashing_HotspotStubSet_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t (class in pyrosetta.rosetta.std) multimap_double_std_shared_ptr_protocols_hotspot_hashing_HotspotStub_t (class in pyrosetta.rosetta.std) MultiObjective (class in pyrosetta.rosetta.protocols.mpi_refinement) MultiPhosphateSampler (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) multiple (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesMode attribute) MultipleDomainMover (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) MultipleOutputSpecification (class in pyrosetta.rosetta.protocols.jd3.output) MultipleOutputter (class in pyrosetta.rosetta.protocols.jd3.output) MultipleOutputWrapper (class in pyrosetta.rosetta.protocols.rosetta_scripts) MultipleOutputWrapperCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) MultiplePoseMover (class in pyrosetta.rosetta.protocols.rosetta_scripts) MultiplePoseMoverCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) MultipleSigmoids (class in pyrosetta.rosetta.protocols.calc_taskop_filters) MultipleSigmoidsFilterCreator (class in pyrosetta.rosetta.protocols.calc_taskop_filters) MultiplexedAnnealableGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) multiplication_dimension() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) multiplicity() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.GenTorsionParams method) (pyrosetta.rosetta.core.scoring.SpringParams method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams method) MULTIPLY_SYMBOL (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) MultiplyExpression (class in pyrosetta.rosetta.numeric.expression_parser) multipole_elec (pyrosetta.rosetta.core.scoring.ScoreType attribute) multipole_elec_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) MULTIPOLE_ELEC_ROTAMER_SET_INFO (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) MULTIPOLE_ENERGIES (pyrosetta.rosetta.basic.ProfTag attribute) MULTIPOLE_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) MULTIPOLE_SETUP (pyrosetta.rosetta.basic.ProfTag attribute) MultipoleAxisType (class in pyrosetta.rosetta.core.scoring) MultipoleElecEnergy (class in pyrosetta.rosetta.core.energy_methods) MultipoleElecEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) MultipoleElecPoseInfo (class in pyrosetta.rosetta.core.scoring) MultipoleElecPotential (class in pyrosetta.rosetta.core.scoring) MultipoleElecResidueInfo (class in pyrosetta.rosetta.core.scoring) MultipoleElecRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) MultipoleParameter (class in pyrosetta.rosetta.core.scoring) MultiProbePerSphereAccumulator (class in pyrosetta.rosetta.core.scoring.packstat) MultiProbePoseAccumulator (class in pyrosetta.rosetta.core.scoring.packstat) MultiStateAggregateFunction (class in pyrosetta.rosetta.protocols.multistate_design) MultistateAggregateFunction (class in pyrosetta.rosetta.protocols.pack_daemon) MultiStateEntity (class in pyrosetta.rosetta.protocols.multistate_design) MultiStateFitnessFunction (class in pyrosetta.rosetta.protocols.multistate_design) MultistateFitnessFunction (class in pyrosetta.rosetta.protocols.pack_daemon) MultiStatePacker (class in pyrosetta.rosetta.protocols.multistate_design) MultiTemperatureTrialCounter (class in pyrosetta.rosetta.protocols.canonical_sampling) MultiThreadingJob (class in pyrosetta.rosetta.protocols.jd2) MultiThreadingMover (class in pyrosetta.rosetta.protocols.comparative_modeling) multivec2poseBfacts() (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) multstubs() (in module pyrosetta.rosetta.protocols.sic_dock) MUST_CONTROL (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength attribute) (pyrosetta.rosetta.protocols.environment.claims.ClaimStrength.PrioSubtype attribute) (pyrosetta.rosetta.protocols.environment.claims.ControlStrength attribute) must_switch_bins() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) MUT_COMPLEXES_LIST_FILE (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData.DDG_Bind_File_Index attribute) mut_resid (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info property) mut_residue() (pyrosetta.rosetta.protocols.pmut_scan.MutationData method) mut_target (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info property) MUT_UNBOUNDS_LIST_FILE (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData attribute) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData.DDG_Bind_File_Index attribute) MutableCache_const_core_chemical_ResidueTypeSet__star__core_pack_palette_BaseTypeList_t (class in pyrosetta.rosetta.utility.thread) MutableChiRecord (class in pyrosetta.rosetta.core.chemical) MutableICoorRecord (class in pyrosetta.rosetta.core.chemical) MutableResidueConnection (class in pyrosetta.rosetta.core.chemical) MutableResidueType (class in pyrosetta.rosetta.core.chemical) Mutant (class in pyrosetta.rosetta.protocols.pmut_scan) mutant_score_components() (pyrosetta.rosetta.protocols.ddg.ddGMover method) MutantPosition (class in pyrosetta.rosetta.protocols.antibody.design) mutants_allowed_ (pyrosetta.rosetta.protocols.antibody.design.MutantPosition property) mutate() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) Mutate1Randomizer (class in pyrosetta.rosetta.protocols.genetic_algorithm) mutate_all_at_once() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) mutate_and_relax() (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) mutate_disulfides_to_ala() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) mutate_loops_for_search() (in module pyrosetta.rosetta.protocols.motifs) mutate_pose() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) mutate_position() (in module pyrosetta.rosetta.core.pose.rna) mutate_position_vector_for_search() (in module pyrosetta.rosetta.protocols.motifs) mutate_res_if_allowed() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) mutate_residue() (in module pyrosetta.toolbox.mutants) mutate_sequence() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) mutate_to_ala_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) MutateFrameworkForCluster (class in pyrosetta.rosetta.protocols.antibody.design) MutateFrameworkForClusterCreator (class in pyrosetta.rosetta.protocols.antibody.design) MutateResidue (class in pyrosetta.rosetta.protocols.simple_moves) MutateResidueCreator (class in pyrosetta.rosetta.protocols.simple_moves) MUTATION (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) mutation_ddGs() (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) mutation_label() (pyrosetta.rosetta.protocols.ddg.ddGMover method) mutation_rate() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.Mutate1Randomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) mutation_string() (pyrosetta.rosetta.protocols.pmut_scan.MutationData method) mutation_string_PDB_numbering() (pyrosetta.rosetta.protocols.pmut_scan.MutationData method) mutation_threshold() (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) MutationData (class in pyrosetta.rosetta.protocols.pmut_scan) mutations() (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) MutationSet (class in pyrosetta.rosetta.protocols.ddg.CartesianddG) MutationSetDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) MutationsFilter (class in pyrosetta.rosetta.protocols.simple_filters) MutationsFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) muted (pyrosetta.rosetta.basic.TracerOptions property) mxr_ (pyrosetta.rosetta.core.scoring.packstat.Octree2D property) mxx_ (pyrosetta.rosetta.core.scoring.packstat.Octree2D property) mxy_ (pyrosetta.rosetta.core.scoring.packstat.Octree2D property) my_group() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) my_group_members() (pyrosetta.rosetta.core.scoring.MultipoleParameter method) my_lk_fraction() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) my_local_coord_frame() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) my_residue_pair_energy() (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) my_setup_for_scoring_for_residue() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) mysql (pyrosetta.rosetta.utility.sql_database.DatabaseMode attribute) (pyrosetta.rosetta.utility.sql_database.DatabaseMode.e attribute) MyTemplatePointerHash1_core_conformation_Residue_t (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) MyWaterHolder (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome)