Index – M

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) 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) 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_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.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) mainchain_dihedral_values() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) mainchain_potentials_match() (pyrosetta.rosetta.core.chemical.ResidueType method) mainchain_torsion() (pyrosetta.rosetta.core.conformation.Residue method) mainchain_torsions() (pyrosetta.rosetta.core.conformation.Residue method) MainChainTorsionSet (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein) make() (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.MakeCSScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeConstScore 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.MakePCS_FragDistance method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePartialSecondarySimilarity 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.MakeProlinePhiScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakePsi method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRDCScore method) (pyrosetta.rosetta.protocols.frag_picker.scores.MakeRamaScore 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_asymmetric_movemap() (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer 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_mutation() (in module pyrosetta.rosetta.protocols.motifs) make_centroid() (in module pyrosetta.rosetta.core.chemical) 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_coarse_pose() (in module pyrosetta.rosetta.protocols.rna.denovo) 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_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.protocols.rna.denovo) 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_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) make_move() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover 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) make_mutation() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) make_new_grid() (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridSet 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_phosphate_nomenclature_matches_mini() (in module pyrosetta.rosetta.core.pose.rna) make_points() (in module pyrosetta.rosetta.numeric.kdtree) 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_residue_mask_symmetric() (in module pyrosetta.rosetta.core.pose.symmetry) make_score_function_consistent_with_symmetric_state_of_pose() (in module pyrosetta.rosetta.core.pose.symmetry) make_segtag_with_dashes() (in module pyrosetta.rosetta.utility) make_semisymmetric_movemap() (pyrosetta.rosetta.core.optimization.symmetry.SymAtomTreeMinimizer method) make_sequence_shift() (pyrosetta.rosetta.protocols.loops.Loops method) make_simple_fold_tree_from_jump_frame() (in module pyrosetta.rosetta.core.fragment) make_specific_mutant() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) 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_tag() (in module pyrosetta.rosetta.utility) make_tag_with_dashes() (in module pyrosetta.rosetta.utility) 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) MakeAtomPairConstraintsScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeBFactor (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeCanonicalHelix (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) MakeLAMBEGO_Similarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) 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) 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) MakeRotLibJobInputter (class in pyrosetta.rosetta.protocols.make_rot_lib) MakeRotLibOptionsData (class in pyrosetta.rosetta.protocols.make_rot_lib) 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) MakeTalosSSSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) MakeTorsionBinSimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) manager() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) manager_type() (pyrosetta.rosetta.protocols.jd2.JD2ResourceManagerCreator method) manipulate_cut_bias() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) map() (pyrosetta.rosetta.basic.datacache.CacheableStringFloatMap method) (pyrosetta.rosetta.basic.datacache.CacheableStringMap method) (pyrosetta.rosetta.core.id.CacheableAtomID_MapVector method) map_char_to_torsion_bin() (in module pyrosetta.rosetta.core.conformation) map_constraints_from_original_pose() (in module pyrosetta.rosetta.core.scoring.constraints) map_from_spectrum() (pyrosetta.rosetta.protocols.electron_density.DockIntoDensityMover method) map_of_weighted_scores() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) map_residues() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) map_seq1_seq2() (in module pyrosetta.rosetta.core.sequence) map_string_to_torsion_bin_string() (in module pyrosetta.rosetta.core.conformation) map_torsion_bin_to_char() (in module pyrosetta.rosetta.core.conformation) mapfile_activated() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) mapping() (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) mapping_to_alignment() (in module pyrosetta.rosetta.core.sequence) mark() (pyrosetta.rosetta.protocols.pockets.ComparisonGrid method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid 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_test_run() (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) mark_connect_incomplete() (pyrosetta.rosetta.core.conformation.Residue method) mark_current_job_id_for_repetition() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) mark_designable() (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread 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.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) mark_energy_uncomputed() (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) mark_incomplete() (pyrosetta.rosetta.core.chemical.ResConnID method) mark_job_tag_as_complete() (pyrosetta.rosetta.basic.resource_manager.LazyResourceManager method) (pyrosetta.rosetta.protocols.jd2.JD2ResourceManager method) mark_leave_as_is() (pyrosetta.rosetta.protocols.toolbox.task_operations.DatabaseThread method) mark_residue_moved() (pyrosetta.rosetta.core.kinematics.ResidueCoordinateChangeList method) mark_tags() (pyrosetta.rosetta.protocols.toolbox.KClusterData method) markDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) markEdgeDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) markOneEdgeDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) markPocketDepth() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) mask_asu() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) mass() (in module pyrosetta.rosetta.core.pose) (pyrosetta.rosetta.core.chemical.ResidueType method) match() (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) 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_dspos1 (class in pyrosetta.rosetta.protocols.match) match_possible_for_hit_geometry() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) match_variants() (pyrosetta.rosetta.core.chemical.ResidueTypeSelector method) MatchConstraintFileInfoList (class in pyrosetta.rosetta.protocols.toolbox.match_enzdes_util) MatchCounter (class in pyrosetta.rosetta.protocols.match) matched_tags() (pyrosetta.rosetta.core.io.silent.SilentFileData method) Matcher (class in pyrosetta.rosetta.protocols.match) MatchPositionModifier (class in pyrosetta.rosetta.protocols.match) MatchScoreWriter (class in pyrosetta.rosetta.protocols.match.output) MatrixMult() (in module pyrosetta.rosetta.numeric.model_quality) 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.numeric.random.RandomGenerator method) max_accepted_trials() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) max_allowed_oversaturated() (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter 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_atomic_interaction_cutoff() (pyrosetta.rosetta.core.scoring.ScoreFunction method) max_atomic_interaction_distance() (pyrosetta.rosetta.core.scoring.ScoreFunctionInfo method) max_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) max_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) 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.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) max_dis2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) max_dist() (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) max_distance() (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator 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) 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_iter() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) max_length() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) max_linear_chainbreak() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover 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_index() (in module pyrosetta.rosetta.protocols.jd2) max_occurs() (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) max_per_move_torsion_delta_per_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) max_pos() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) max_rad() (in module pyrosetta.rosetta.core.scoring.packstat) max_rms() (pyrosetta.rosetta.protocols.loophash.FastGapMover method) max_rotbump_energy() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ 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_score_diffs() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter 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.SecMatchResiduePairEvaluator method) max_size() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) max_size_col() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) max_total_torsion_delta_per_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) max_tries_multiplier_for_ccd() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) max_valence_electrons_sp() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) max_values() (pyrosetta.rosetta.numeric.kdtree.KDPointList method) maxcycles() (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) maxtrials() (pyrosetta.rosetta.protocols.simple_moves.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.AppendMainchainAtom 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.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.SetAllAtomsRepulsive method) (pyrosetta.rosetta.core.chemical.SetAtomType method) (pyrosetta.rosetta.core.chemical.SetAtomicCharge method) (pyrosetta.rosetta.core.chemical.SetBackboneHeavyatom method) (pyrosetta.rosetta.core.chemical.SetFormalCharge method) (pyrosetta.rosetta.core.chemical.SetICoor method) (pyrosetta.rosetta.core.chemical.SetIO_String method) (pyrosetta.rosetta.core.chemical.SetInterchangeabilityGroup_String method) (pyrosetta.rosetta.core.chemical.SetMMAtomType method) (pyrosetta.rosetta.core.chemical.SetNbrAtom method) (pyrosetta.rosetta.core.chemical.SetNbrRadius 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) mc() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) MC() (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) mc() (pyrosetta.rosetta.protocols.moves.TrialMover method) mc_accepted() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) mc_accepted_string() (pyrosetta.rosetta.protocols.moves.MonteCarlo method) mc_accpeted() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) mcfi() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfoList method) mean() (in module pyrosetta.rosetta.numeric) mean_and_stdev() (in module pyrosetta.rosetta.protocols.mpi_refinement) mean_squared_error() (pyrosetta.rosetta.numeric.MultiDimensionalHistogram method) MeanField (class in pyrosetta.rosetta.protocols.mean_field) measure_rotamer_recovery() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) Medal_main() (in module pyrosetta.rosetta.protocols.medal) MedalExchange_main() (in module pyrosetta.rosetta.protocols.medal) MedalMover (class in pyrosetta.rosetta.protocols.medal) median() (in module pyrosetta.rosetta.numeric) meets_requirements() (pyrosetta.rosetta.core.chemical.Metapatch method) 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.LoopHashMap method) mem_footprint() (pyrosetta.rosetta.core.io.silent.SilentStruct 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_bbGauss method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) mem_pair_log() (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) memb_dsolv1() (pyrosetta.rosetta.core.scoring.etable.MembEtable method) memb_dsolv2() (pyrosetta.rosetta.core.scoring.etable.MembEtable 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) Membed_init() (pyrosetta.rosetta.core.scoring.MembranePotential method) member_constraints() (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) MembEtable (class in pyrosetta.rosetta.core.scoring.etable) 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_FAEmbed (class in pyrosetta.rosetta.core.scoring) Membrane_FAEmbed_from_pose() (in module pyrosetta.rosetta.core.scoring) Membrane_FAPotential (class in pyrosetta.rosetta.core.scoring) membrane_info() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation 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_steepness() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) membrane_thickness() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) MembraneAbinitio (class in pyrosetta.rosetta.protocols.abinitio) 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) MembraneInfo (class in pyrosetta.rosetta.core.conformation.membrane) 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) MembraneTopology (class in pyrosetta.rosetta.protocols.simple_moves) MembraneTopology_from_pose() (in module pyrosetta.rosetta.core.scoring) memory_use() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) Menv_penalties() (pyrosetta.rosetta.core.scoring.MembranePotential method) 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.ScoreFunction method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.wum.WorkUnitList method) merge_behavior_manager() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet 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_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_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) merged() (pyrosetta.rosetta.utility.options.OptionCollection method) 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) MetalContactsConstraintGenerator (class in pyrosetta.rosetta.protocols.constraint_generator) 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) metapatches() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) method_type() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) method_weights() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) metric() (pyrosetta.rosetta.core.pose.Pose method) MetricRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) MetricRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) metropolis_hastings_mover() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover 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.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover 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) MetropolisHastingsMover (class in pyrosetta.rosetta.protocols.canonical_sampling) MetropolisHastingsMoverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) mg_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) mid_pos() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop 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() (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.numeric.random.RandomGenerator method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) min_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) min_bb() (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.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover 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) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) min_bb_set() (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.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover 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) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) min_bond_length() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) min_c_terminal_charges() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) min_client_rank() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) min_dis() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) min_dis2() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) min_dist() (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) min_distance() (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) min_heap() (pyrosetta.rosetta.protocols.cluster.Exemplar method) min_helix_length() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) min_length() (pyrosetta.rosetta.protocols.antibody.CDRSetOptions method) min_mod() (in module pyrosetta.rosetta.protocols.cryst) 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.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) min_options() (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) min_pack() (in module pyrosetta.rosetta.core.pack) 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_pos() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) min_rb() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions 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.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover 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) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) min_rb_set() (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.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover 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) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) min_rms() (pyrosetta.rosetta.protocols.loophash.FastGapMover method) min_rotamers() (in module pyrosetta.rosetta.protocols.make_rot_lib) min_sc() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions 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.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover 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) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) min_sc_set() (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.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover 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) (pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover method) min_symm_dist2() (pyrosetta.rosetta.protocols.electron_density.DensitySymmInfo method) min_tolerance() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) min_type() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) mini_pose_list() (pyrosetta.rosetta.protocols.rna.denovo.libraries.BasePairStepLibrary method) minimization_graph() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies 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) minimize_after_delete() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) minimize_all() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) minimize_and_score_native_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) minimize_and_score_sugar() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) minimize_bond_angles() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) minimize_bond_lengths() (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) minimize_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) minimize_in_whole_structure_context() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) minimize_interface() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) minimize_magnesium_and_hydration_shell() (in module pyrosetta.rosetta.protocols.magnesium) minimize_no_bb() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) minimize_waters() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) minimize_with_constraints() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) MinimizeInterface() (in module pyrosetta.rosetta.protocols.protein_interface_design) Minimizer (class in pyrosetta.rosetta.core.optimization) minimizer_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) minimizer_rename_tag() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) MinimizeStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) MiniPose (class in pyrosetta.rosetta.core.pose) minirosetta_svn_url() (in module pyrosetta.rosetta.core) minirosetta_svn_version() (in module pyrosetta.rosetta.core) MinMover (class in pyrosetta.rosetta.protocols.simple_moves) MinPackMover (class in pyrosetta.rosetta.protocols.simple_moves) mintype() (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptions method) minus_minus() (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) mirror_symm() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) mirror_symmetry() (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) mirrored_relative_to_type() (pyrosetta.rosetta.core.conformation.Residue method) MirrorSymmetricConformation (class in pyrosetta.rosetta.core.conformation.symmetry) missing_atoms() (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) missing_dens_as_jump() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) missing_in_pose() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintParameters method) MixtureFunc (class in pyrosetta.rosetta.core.scoring.func) MKDIR() (in module pyrosetta.rosetta.protocols.sparta) 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) mm_atom_type_index() (pyrosetta.rosetta.core.chemical.Atom 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.ResidueType method) mm_bond_angle_residue_type_param_set() (in module pyrosetta.rosetta.core.scoring.mm) mm_from_residues() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) mm_lj_library() (pyrosetta.rosetta.core.scoring.mm.MMLJScore method) mm_lj_score() (pyrosetta.rosetta.core.scoring.mm.MMLJEnergyTable method) mm_name() (pyrosetta.rosetta.core.chemical.Atom method) mm_type() (pyrosetta.rosetta.core.conformation.Atom method) MMAtomType (class in pyrosetta.rosetta.core.chemical) MMAtomTypeSet (class in pyrosetta.rosetta.core.chemical) MMBondAngleScore (class in pyrosetta.rosetta.core.scoring.mm) mmCIFJobOutputter (class in pyrosetta.rosetta.protocols.jd2) mmf_cat_in_datamap() (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) mmf_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader method) MMLJEnergyTable (class in pyrosetta.rosetta.core.scoring.mm) MMLJLibrary (class in pyrosetta.rosetta.core.scoring.mm) MMLJScore (class in pyrosetta.rosetta.core.scoring.mm) MMTorsionLibrary (class in pyrosetta.rosetta.core.scoring.mm) MMTorsionScore (class in pyrosetta.rosetta.core.scoring.mm) MNBRAK() (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) mod() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.ObjexxFCL) mode() (pyrosetta.rosetta.core.chemical.AtomTypeSet method) (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.residue_selectors.UnsatSelector method) model() (pyrosetta.rosetta.protocols.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_h3() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) model_ids() (pyrosetta.rosetta.protocols.sewing.Assembly method) (pyrosetta.rosetta.protocols.sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.sewing.DisembodiedAssembly method) model_resnum() (pyrosetta.rosetta.protocols.sewing.HashEdge method) ModelCDRH3 (class in pyrosetta.rosetta.protocols.antibody) 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) ModelFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ModelNode (class in pyrosetta.rosetta.protocols.sewing) 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.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) modified2original_interval_endpoints() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) 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) ModifiedResidueInformation (class in pyrosetta.rosetta.core.io) 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.toolbox.task_operations.ProteinInterfaceDesignOperation method) modify_atom_properties_from_command_line() (in module pyrosetta.rosetta.core.chemical) modify_before_jump() (pyrosetta.rosetta.protocols.toolbox.task_operations.ProteinInterfaceDesignOperation method) modify_ft_for_residue_insertion() (in module pyrosetta.rosetta.protocols.denovo_design.components) modify_impl() (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) modify_relative_filters_pdb_names() (pyrosetta.rosetta.protocols.simple_filters.Operator method) modify_task() (pyrosetta.rosetta.core.pack.task.TaskFactory method) modify_unselected_residues() (pyrosetta.rosetta.protocols.toolbox.task_operations.SelectResiduesWithinChainOperation method) 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) ModifyStoredRBConfs (class in pyrosetta.rosetta.protocols.enzdes) ModifyVariantTypeMover (class in pyrosetta.rosetta.protocols.simple_moves) modp() (in module pyrosetta.rosetta.numeric.kinematic_closure) modres_map() (pyrosetta.rosetta.core.io.StructFileRep method) modrf() (in module pyrosetta.rosetta.numeric.kinematic_closure) modulo() (in module pyrosetta.rosetta.numeric) (in module pyrosetta.rosetta.utility) MolecularSurfaceCalculator (class in pyrosetta.rosetta.core.scoring.sc) moltenres() (pyrosetta.rosetta.protocols.hbnet.HBondNode method) moltenres_atomtree_collection() (pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection method) momento_for_moltenres() (pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment method) monopole() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) monte_carlo() (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController 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) monte_carlo_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.MonteCarloLoader method) MonteCarlo (class in pyrosetta.rosetta.protocols.moves) MonteCarloLoader (class in pyrosetta.rosetta.protocols.parser) MonteCarloUtil (class in pyrosetta.rosetta.protocols.moves) more_precise_base_pair_classification() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) morpheme_from_ring_size() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) most_probable_bin() (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) motif2scaffold_data (class in pyrosetta.rosetta.protocols.motif_grafting.movers) motif2scaffold_indexes (class in pyrosetta.rosetta.protocols.motif_grafting.movers) motifs_begin() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) motifs_end() (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoMotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) movable_group() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) movable_jumps() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation 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_element() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) move_jumps_between_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions 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.protocols.simple_moves.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.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) move_together() (in module pyrosetta.rosetta.protocols.docking) move_type() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) move_type_from_string() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) moveable_jump() (in module pyrosetta.rosetta.protocols.rna.denovo) MoveBeforeFilter (class in pyrosetta.rosetta.protocols.filters) moved() (pyrosetta.rosetta.core.scoring.EnergyNode method) MoveMap (class in pyrosetta.rosetta.core.kinematics) movemap() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio 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.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover 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.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) movemap_as_OP() (pyrosetta.rosetta.protocols.forge.build.BuildManager method) movemap_builder_ct_namer() (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader 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_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.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover 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) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) movemap_factory_category() (in module pyrosetta.rosetta.core.select.movemap) movemap_from_blueprint() (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) movemap_torsion_id_begin() (pyrosetta.rosetta.core.kinematics.MoveMap method) movemap_torsion_id_end() (pyrosetta.rosetta.core.kinematics.MoveMap method) MoveMapBuilderLoader (class in pyrosetta.rosetta.protocols.ligand_docking) MoveMapFactoryLoader (class in pyrosetta.rosetta.protocols.parser) MovePoseToMembraneCenterMover (class in pyrosetta.rosetta.protocols.rigid) mover() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) mover_name() (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignProtocol method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanRelaxMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeRelax method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.fold_from_loops.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.RotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover 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.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover 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.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation 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.SetAtomTree method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CstInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MinMover method) (pyrosetta.rosetta.protocols.simple_moves.MinPackMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover method) (pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.simple_moves.PertMinMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SaneMinMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins 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.SetChiMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.toolbox.task_operations.StoreTaskMover method) mover_or_add_group_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) mover_tag() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) mover_weight() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) MoverCreator (class in pyrosetta.rosetta.protocols.moves) movers() (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) MoverStatus (class in pyrosetta.rosetta.protocols.moves) moves_residue() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) moving_res() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMove method) mp_param() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) MPCbetaEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPCbetaEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) 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) MPEnvEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPEnvEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPFastRelaxMoverCreator (class in pyrosetta.rosetta.protocols.relax.membrane) MPFindInterfaceMoverCreator (class in pyrosetta.rosetta.protocols.docking.membrane) MPI_FILE_STATUS (class in pyrosetta.rosetta.utility.io.mpi_stream) mpi_finalize() (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIFileBufJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIMultiCommJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPartitionJobDistributor method) (pyrosetta.rosetta.protocols.jd2.MPIWorkPoolJobDistributor method) mpi_npes() (in module pyrosetta.rosetta.protocols.wum) mpi_nprocs() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) mpi_rank() (in module pyrosetta.rosetta.protocols.wum) (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.utility.SimulateMPI method) MPI_ranks_handling_message() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_JobResultsSummary method) MPI_reroute_rank() (pyrosetta.rosetta.utility.io.ozstream method) mpi_safe_std_err() (in module pyrosetta.rosetta.utility.options) MPI_STREAM_MSG (class in pyrosetta.rosetta.utility.io.mpi_stream) MPIArchiveJobDistributor (class in pyrosetta.rosetta.protocols.jd2.archive) MPIFileBufJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPIMultiCommJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPIWorkPartitionJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPIWorkPoolJobDistributor (class in pyrosetta.rosetta.protocols.jd2) MPLipidAccessibility (class in pyrosetta.rosetta.protocols.membrane) MPLipoEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPLipoEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPMutateRelaxMoverCreator (class in pyrosetta.rosetta.protocols.membrane) MPNonHelixPenalty (class in pyrosetta.rosetta.core.scoring.membrane) MPNonHelixPenaltyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPPairEnergy (class in pyrosetta.rosetta.core.scoring.membrane) MPPairEnergyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPQuickRelaxMoverCreator (class in pyrosetta.rosetta.protocols.membrane) MPSymDockMoverCreator (class in pyrosetta.rosetta.protocols.symmetric_docking.membrane) MPTerminiPenalty (class in pyrosetta.rosetta.core.scoring.membrane) MPTerminiPenaltyCreator (class in pyrosetta.rosetta.core.scoring.membrane) MPTMProjPenalty (class in pyrosetta.rosetta.core.scoring.membrane) MPTMProjPenaltyCreator (class in pyrosetta.rosetta.core.scoring.membrane) msg() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds 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.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.utility.excn.EXCN_BadInput method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) mstype_from_name() (in module pyrosetta.rosetta.protocols.moves) mu() (pyrosetta.rosetta.core.pose.Pose method) MulliganPNearEvaluator (class in pyrosetta.rosetta.protocols.toolbox) 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_relative() (pyrosetta.rosetta.protocols.simple_filters.Operator method) multi_use() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) MultiConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) MultiDimensionalHistogram (class in pyrosetta.rosetta.numeric) Multifunc (class in pyrosetta.rosetta.core.optimization) MultipleDomainMover (class in pyrosetta.rosetta.protocols.rna.denovo.coarse) MultipleSigmoids (class in pyrosetta.rosetta.protocols.simple_filters) MultipoleAxisType (class in pyrosetta.rosetta.core.scoring) MultipoleElecPoseInfo (class in pyrosetta.rosetta.core.scoring) MultipoleElecResidueInfo (class in pyrosetta.rosetta.core.scoring) MultipoleElecRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) MultiStatePacker (class in pyrosetta.rosetta.protocols.multistate_design) MultiTemperatureTrialCounter (class in pyrosetta.rosetta.protocols.canonical_sampling) multivec2poseBfacts() (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) multstubs() (in module pyrosetta.rosetta.protocols.sic_dock) must_switch_bins() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) mutants_begin() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) mutants_end() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) mutate() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) mutate_all_at_once() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) mutate_loops_for_search() (in module pyrosetta.rosetta.protocols.motifs) 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) MutateFrameworkForCluster (class in pyrosetta.rosetta.protocols.antibody.design) MutateResidue (class in pyrosetta.rosetta.protocols.simple_moves) mutation_ddGs() (pyrosetta.rosetta.core.io.PositionDdGInfo.PositionDdGInfo method) mutation_rate() (pyrosetta.rosetta.protocols.genetic_algorithm.DiscreteRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityRandomizer method) (pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer method) MutationSetDesignOperation (class in pyrosetta.rosetta.protocols.toolbox.task_operations) my_group() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) my_itr() (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) my_local_coord_frame() (pyrosetta.rosetta.core.scoring.MultipoleElecResidueInfo method) my_residue_pair_energy() (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method)