Index – P

p (class in pyrosetta.rosetta.numeric.kinematic_closure) P (pyrosetta.rosetta.core.chemical.element.Elements attribute) p (pyrosetta.rosetta.protocols.environment.claims.CutBiasElement property) (pyrosetta.rosetta.protocols.environment.claims.CutElement property) (pyrosetta.rosetta.protocols.forge.build.CountFromLeft property) (pyrosetta.rosetta.protocols.sic_dock.Rose property) p0() (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) p1 (pyrosetta.rosetta.protocols.environment.claims.JumpElement property) p1() (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) p1_deriv() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) p1_theta_deriv() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint static method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint static method) p2 (pyrosetta.rosetta.protocols.environment.claims.JumpElement property) p2_deriv() (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) p_ (pyrosetta.rosetta.core.optimization.Particle property) P_AA (class in pyrosetta.rosetta.core.scoring) p_aa (pyrosetta.rosetta.core.scoring.ScoreType attribute) P_aa1 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_aa2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_AA_ABEGO3 (class in pyrosetta.rosetta.core.scoring) P_AA_ABEGO3_energy() (pyrosetta.rosetta.core.scoring.P_AA_ABEGO3 method) P_AA_Energy (class in pyrosetta.rosetta.core.energy_methods) P_AA_energy() (pyrosetta.rosetta.core.scoring.P_AA method) P_AA_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) p_aa_pp (pyrosetta.rosetta.core.scoring.ScoreType attribute) P_AA_pp_Energy (class in pyrosetta.rosetta.core.energy_methods) P_AA_pp_energy() (pyrosetta.rosetta.core.scoring.P_AA method) P_AA_pp_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) p_aa_pp_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) P_AA_ss (class in pyrosetta.rosetta.core.scoring) p_aa_ss (pyrosetta.rosetta.core.scoring.ScoreType attribute) P_AA_ss_Energy (class in pyrosetta.rosetta.core.energy_methods) P_AA_ss_energy() (pyrosetta.rosetta.core.scoring.P_AA_ss method) P_AA_ss_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) p_atom_index() (pyrosetta.rosetta.core.chemical.rna.RNA_Info method) p_atom_index_ (pyrosetta.rosetta.core.chemical.rna.RNA_Info property) P_coorderr (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_dssp1 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_dssp2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_faatr (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_faatr_or_hb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_faatr_or_hbbb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_hb_bb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_hb_bb_sc (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_hb_sc (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) p_i_given_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) p_iplus1_given_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) P_lig (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_max_seqsep (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_maxdist2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_mindist2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_no_hb_bb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_nodisulf (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_noloops (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_not_restype (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_not_restype_one (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_occupancy (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_omega0() (in module pyrosetta.rosetta.numeric.crick_equations) P_oneloop (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_pdb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_restype (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_restype1 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_restype2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_restype_one (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_score (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_seqsep (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_ss1 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_ss2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_type_BB_BB (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_type_BB_PH (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_type_BB_PO (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_type_PH_PO (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_type_SC_BB (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_type_SC_PH (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_type_SC_PO (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_type_SC_SC (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) P_uniformfrag (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) p_value() (pyrosetta.rosetta.protocols.frag_picker.scores.AdaptiveScoreHistogram method) Pa (pyrosetta.rosetta.core.chemical.element.Elements attribute) paa_abego3 (pyrosetta.rosetta.core.scoring.ScoreType attribute) PACK (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) pack() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) pack_all_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) pack_anchor() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) pack_and_minimize() (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) pack_and_minimize_linker_and_sidechains() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) pack_extra_bodies() (in module pyrosetta.rosetta.protocols.chemically_conjugated_docking) pack_missing_sidechains() (in module pyrosetta.rosetta.core.pack) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) pack_o2prime_hydrogens() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) pack_phosphate_penalty() (pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options method) pack_polar_hydrogens() (in module pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens) pack_protein_side_chains() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) pack_residue() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) pack_result() (in module pyrosetta.distributed.packed_pose.core) PACK_ROTAMERS (pyrosetta.rosetta.basic.ProfTag attribute) pack_rotamers() (in module pyrosetta.rosetta.core.pack) pack_rotamers_cleanup() (in module pyrosetta.rosetta.core.pack) pack_rotamers_loop() (in module pyrosetta.rosetta.core.pack) pack_rotamers_run() (in module pyrosetta.rosetta.core.pack) pack_rotamers_setup() (in module pyrosetta.rosetta.core.pack) pack_scorefxn_pose_handshake() (in module pyrosetta.rosetta.core.pack) pack_stat (pyrosetta.rosetta.core.scoring.ScoreType attribute) pack_weights() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) PACKABLE (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation attribute) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerSpecificationType attribute) packable() (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) package() (pyrosetta.rosetta.utility.Version static method) packcycles (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams property) PackDaemon (class in pyrosetta.rosetta.protocols.pack_daemon) packed_residues() (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) packed_rotno() (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_double_t method) (pyrosetta.rosetta.core.pack.dunbrack.PackedDunbrackRotamer_5_5_float_t method) packed_rotno_ (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t property) packed_rotno_2_rotwell() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) PackedDunbrackRotamer_1_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_1_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_1_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_1_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_1_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_1_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_1_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_1_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_1_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_1_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_2_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_3_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_4_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_1_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_1_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_2_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_2_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_3_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_3_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_4_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_4_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_5_double_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedDunbrackRotamer_5_5_float_t (class in pyrosetta.rosetta.core.pack.dunbrack) PackedPose (class in pyrosetta.distributed.packed_pose.core) packer (pyrosetta.rosetta.protocols.electron_density.MinimizePoseIntoDensityOptions property) packer() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWiseMasterPacker method) packer_loop() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) packer_palette() (pyrosetta.rosetta.core.pack.task.TaskFactory method) packer_palette_creator_map() (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) packer_palette_xml_schema_group_name() (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory static method) PackerEnergyAdd() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) PackerEnergyMultiply() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) PackerEnergySubtract() (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) PackerNeighborGraphFilter (class in pyrosetta.rosetta.protocols.simple_filters) PackerPalette (class in pyrosetta.rosetta.core.pack.palette) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) packerpalette_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.PackerPaletteLoaderCreator static method) PackerPaletteCreator (class in pyrosetta.rosetta.core.pack.palette) PackerPaletteFactory (class in pyrosetta.rosetta.core.pack.palette) PackerPaletteLoader (class in pyrosetta.rosetta.protocols.parser) PackerPaletteLoaderCreator (class in pyrosetta.rosetta.protocols.parser) PackerTask (class in pyrosetta.rosetta.core.pack.task) packertask() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) PackerTask_ (class in pyrosetta.rosetta.core.pack.task) PackerTaskSymmetryStatus (class in pyrosetta.rosetta.core.pack.task) packeruser() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) packing_angle_degrees_ (pyrosetta.rosetta.protocols.legacy_sewing.Model property) packing_angle_enum_to_string() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) packing_angle_string_to_enum() (pyrosetta.rosetta.protocols.antibody.AntibodyEnumManager method) packing_correction() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) packing_interaction_cutoff() (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) packing_shell() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) PackingAngleEnum (class in pyrosetta.rosetta.protocols.antibody) PackingAngleEnum_start (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) PackingAngleEnum_total (pyrosetta.rosetta.protocols.antibody.PackingAngleEnum attribute) PackingScore (class in pyrosetta.rosetta.core.scoring.packstat) PackingScoreResData (class in pyrosetta.rosetta.core.scoring.packstat) PackingState (class in pyrosetta.rosetta.protocols.multistate_design) PackRotamersMover (class in pyrosetta.rosetta.protocols.minimization_packing) PackRotamersMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) PackRotamersMoverLazy (class in pyrosetta.rosetta.protocols.minimization_packing) PackRotamersMoverLazyCreator (class in pyrosetta.rosetta.protocols.minimization_packing) PackRotamersMoverPartGreedy (class in pyrosetta.rosetta.protocols.enzdes) PackRotamersMoverPartGreedyCreator (class in pyrosetta.rosetta.protocols.enzdes) PackScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) packstat (pyrosetta.rosetta.protocols.analysis.InterfaceData property) PackstatCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) PackStatEnergy (class in pyrosetta.rosetta.core.energy_methods) PackStatEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) PackStatFilter (class in pyrosetta.rosetta.protocols.simple_filters) PackStatFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) PackStatMover (class in pyrosetta.rosetta.protocols.analysis) pad() (in module pyrosetta.rosetta.ObjexxFCL) pad_atom_name() (in module pyrosetta.rosetta.utility) pad_left() (in module pyrosetta.rosetta.utility) pad_results() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Base method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastPlus method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_LoopOverSCs method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_MultiTemplate method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrix method) pad_right() (in module pyrosetta.rosetta.utility) pad_sequences() (in module pyrosetta.rosetta.protocols.pdbinfo_manipulations) padded (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) padded() (in module pyrosetta.rosetta.ObjexxFCL) pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) pair_constel_set() (in module pyrosetta.rosetta.protocols.constel) pair_constel_set_idx2() (in module pyrosetta.rosetta.protocols.constel) pair_e_method (pyrosetta.rosetta.core.scoring.methods.EnergyMethods attribute) pair_energy_H() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) pair_energy_H_v() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.EtableEvaluator method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEvaluator method) pair_has_linkage_statistics() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) Pair_impl_utility_json_spirit_Config_vector_std_string_t (class in pyrosetta.rosetta.utility.json_spirit) pair_list() (pyrosetta.rosetta.protocols.scoring.Interface method) pair_meets_starting_criteria() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) pair_overlap_tolerance() (pyrosetta.rosetta.protocols.match.BumpGrid method) pair_sets_with_positions() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) pair_term_energy() (pyrosetta.rosetta.core.scoring.PairEPotential method) pair_term_energy_and_deriv() (pyrosetta.rosetta.core.scoring.PairEPotential method) pair_term_energy_exists() (pyrosetta.rosetta.core.scoring.PairEPotential method) pair_with_scaffold() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) paircover (pyrosetta.rosetta.core.scoring.motif.MotifHits property) paired() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.protocols.dna.DnaPosition method) PairedSheetResidueSelector (class in pyrosetta.rosetta.protocols.denovo_design.residue_selectors) PairedSheetResidueSelectorCreator (class in pyrosetta.rosetta.protocols.denovo_design.residue_selectors) PairEnergy (class in pyrosetta.rosetta.core.energy_methods) PairEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) PairEPotential (class in pyrosetta.rosetta.core.scoring) PairFeatures (class in pyrosetta.rosetta.protocols.features) PairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) PairFuncMap (class in pyrosetta.rosetta.core.scoring.custom_pair_distance) Pairing (class in pyrosetta.rosetta.core.scoring.dssp) pairing() (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) pairing_group_namer() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect static method) pairing_string() (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) pairing_subelement_ct_namer() (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect static method) PairingLibrary (class in pyrosetta.rosetta.protocols.jumping) pairings() (pyrosetta.rosetta.protocols.abinitio.Templates method) pairings_size() (pyrosetta.rosetta.protocols.jumping.MembraneJump method) PairingStatEntry (class in pyrosetta.rosetta.protocols.abinitio) PairingStatistics (class in pyrosetta.rosetta.protocols.abinitio) PairingTemplate (class in pyrosetta.rosetta.protocols.jumping) pairs() (pyrosetta.rosetta.core.sequence.PairScoringScheme method) PairScoringScheme (class in pyrosetta.rosetta.core.sequence) PalesEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) PalesEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) PARA_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) ParaIon (class in pyrosetta.rosetta.core.io.nmr) PARALLEL (pyrosetta.rosetta.core.chemical.rna.BaseDoubletOrientation attribute) parallel() (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) parallel_base_test() (in module pyrosetta.rosetta.protocols.motifs) ParallelBetaPairingPreferenceFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) ParallelBetaPairingPreferenceFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) ParallelTempering (class in pyrosetta.rosetta.protocols.canonical_sampling) ParallelTemperingCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) param() (pyrosetta.rosetta.core.scoring.packing.HolesParamsRes method) param1 (pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand property) (pyrosetta.rosetta.protocols.relax.RelaxScriptCommand property) param1() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) param2 (pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand property) (pyrosetta.rosetta.protocols.relax.RelaxScriptCommand property) param2() (pyrosetta.rosetta.protocols.branch_angle.BranchAngleOptimizer method) param3 (pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand property) (pyrosetta.rosetta.protocols.relax.RelaxScriptCommand property) param4 (pyrosetta.rosetta.protocols.denovo_design.movers.RelaxScriptCommand property) (pyrosetta.rosetta.protocols.relax.RelaxScriptCommand property) param_cache() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesCstCache method) param_index() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) PARAMAGNETIC (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) ParamagneticDatabaseHandler (class in pyrosetta.rosetta.core.io.nmr) Parameter (class in pyrosetta.rosetta.core.conformation.parametric) parameter() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) parameter_cop() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) parameter_description() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) parameter_description_from_enum() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator static method) parameter_enum_from_name() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator static method) parameter_name() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) parameter_name_from_enum() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator static method) parameter_op() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) parameter_properties_from_enum() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator static method) parameter_set4final() (pyrosetta.rosetta.protocols.hybridization.TMalign method) parameter_set4scale() (pyrosetta.rosetta.protocols.hybridization.TMalign method) parameter_set4search() (pyrosetta.rosetta.protocols.hybridization.TMalign method) parameter_type() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) parameter_type_from_enum() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator static method) parameter_units() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) parameter_units_from_enum() (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator static method) parametercheck_filter() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) ParameterizationCalculatorProperties (class in pyrosetta.rosetta.core.conformation.parametric) Parameters (class in pyrosetta.rosetta.core.conformation.parametric) parameters() (pyrosetta.rosetta.core.conformation.parametric.ParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) (pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix method) parameters_cop() (pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator method) parameters_for_restype() (pyrosetta.rosetta.core.energy_methods.IdealParametersDatabase method) parameters_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) parameters_set() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) parameters_set_index() (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) ParametersSet (class in pyrosetta.rosetta.core.conformation.parametric) ParameterType (class in pyrosetta.rosetta.core.conformation.parametric) ParametrizationCalculator (class in pyrosetta.rosetta.core.conformation.parametric) params_database_tag() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) params_file (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) params_vec (pyrosetta.rosetta.protocols.relax.RelaxScriptCommand property) ParaNMRScoreMover (class in pyrosetta.rosetta.protocols.nmr) ParaNMRScoreMoverCreator (class in pyrosetta.rosetta.protocols.nmr) paratope (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_double_t property) (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_long_t property) paratope_charge() (in module pyrosetta.rosetta.protocols.antibody) paratope_heavy (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_double_t property) (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_long_t property) paratope_light (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_double_t property) (pyrosetta.rosetta.protocols.antibody.ParatopeMetric_long_t property) paratope_sasa() (in module pyrosetta.rosetta.protocols.antibody) ParatopeEpitopeSiteConstraintMover (class in pyrosetta.rosetta.protocols.antibody.constraints) ParatopeEpitopeSiteConstraintMoverCreator (class in pyrosetta.rosetta.protocols.antibody.constraints) ParatopeMetric_double_t (class in pyrosetta.rosetta.protocols.antibody) ParatopeMetric_long_t (class in pyrosetta.rosetta.protocols.antibody) ParatopeSiteConstraintMover (class in pyrosetta.rosetta.protocols.antibody.constraints) ParatopeSiteConstraintMoverCreator (class in pyrosetta.rosetta.protocols.antibody.constraints) parcs_ccs() (in module pyrosetta.rosetta.core.energy_methods) parent (pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms property) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile property) (pyrosetta.rosetta.utility.graph.DS_Node property) parent() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.optimization.DOF_Node method) (pyrosetta.rosetta.numeric.ClusteringTreeNode method) (pyrosetta.rosetta.numeric.kdtree.KDNode method) (pyrosetta.rosetta.protocols.jd3.JGResultNode method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.CoordinateConstraintStack method) (pyrosetta.rosetta.utility.file.PathName method) parent_full_model_parameters() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) parent_id() (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) parent_node() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTarget method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNode method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.InvrotTreeNodeBase method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.SingleResidueInvrotTarget method) parent_segments_ (pyrosetta.rosetta.protocols.legacy_sewing.SewSegment property) parents() (pyrosetta.rosetta.protocols.jd3.JGJobNode method) parin_favorite_output() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) parse() (pyrosetta.rosetta.core.chemical.mmCIF.mmCIFParser method) (pyrosetta.rosetta.core.chemical.sdf.CtabParserBase method) (pyrosetta.rosetta.core.chemical.sdf.CtabV2000Parser method) (pyrosetta.rosetta.core.chemical.sdf.CtabV3000Parser method) (pyrosetta.rosetta.core.chemical.sdf.SDFParser method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTAndClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFactor method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFunction method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTOrClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestAndClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestExpression method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestOrClause method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTRestTerm method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTTerm method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) parse_additional_residue_types() (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) parse_adduct_string() (in module pyrosetta.rosetta.core.chemical) parse_apply_to_pose_tag() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) parse_assembly_scorers() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) parse_atom_pair_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) parse_atom_type_data() (in module pyrosetta.rosetta.core.chemical.sdf) parse_attach_description() (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) parse_attributes_from_tag() (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparer method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerAutomorphicRMSD method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerChiDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerElecDensDiff method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRComparerRotBins method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocol method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMinPack method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolPackRotamers method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolReferenceStructure method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRelax method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRotamerTrials method) (pyrosetta.rosetta.protocols.rotamer_recovery.RRProtocolRTMin method) parse_base_tag() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) parse_batch_description_tag_item() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) parse_batch_id_tag_item() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) parse_batch_name_tag_item() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) parse_boolean() (in module pyrosetta.rosetta.utility) parse_bounds_lines() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) parse_cache_size_tag_item() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) parse_chain_endings() (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) parse_command_line() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) parse_constraint_generators() (in module pyrosetta.rosetta.protocols.constraint_generator) parse_coordinate_constraint() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) parse_custom_torsion() (in module pyrosetta.rosetta.protocols.constraint_generator) parse_data() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) parse_database_connection() (in module pyrosetta.rosetta.basic.database) parse_database_session() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_decay_info_lines() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) parse_decay_lines() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) parse_default_and_user_options() (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser method) parse_desc_lines() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) parse_dist_datatype() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) parse_dist_info_lines() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) parse_dist_lines() (pyrosetta.rosetta.core.scoring.epr_deer.DEERIO method) parse_dof_task_type() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) parse_dof_tasks() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) parse_elazar_polynom_table() (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) parse_elazar_spline_table() (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) parse_energies() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) parse_excluded_properites() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_excluded_types() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_file() (pyrosetta.rosetta.core.chemical.sdf.MolFileIOReader method) parse_filter() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_filter_or_null() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_filter_with_logic() (in module pyrosetta.rosetta.protocols.filters) parse_global_requirements() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) parse_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) parse_gridset_tag() (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader method) parse_ideal_contacts() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer static method) parse_import_tag() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) parse_in_progress() (pyrosetta.rosetta.core.io.HeaderInformation method) parse_included_properites() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_included_types() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_input() (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) parse_intra_segment_requirements() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) parse_jump_selector() (in module pyrosetta.rosetta.core.select.jump_selector) parse_layer_secstruct_tag() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) parse_layer_tag() (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) parse_lengths() (in module pyrosetta.rosetta.protocols.denovo_design.components) parse_ligand_conformers() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) parse_ligand_files() (pyrosetta.rosetta.protocols.sewing.hashing.LigandBindingResPlacer static method) parse_ligands_tag() (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) parse_loops_from_tag() (in module pyrosetta.rosetta.protocols.loop_modeling.utilities) parse_lsm_spec() (pyrosetta.rosetta.protocols.hotspot_hashing.LSMSearchPattern static method) parse_motif() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) parse_motif_file() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) parse_motif_string() (in module pyrosetta.rosetta.protocols.denovo_design) parse_movemap() (pyrosetta.rosetta.protocols.md.CartesianMD method) parse_movemap_factory() (in module pyrosetta.rosetta.core.select.movemap) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) parse_movemap_factory_legacy() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_mover() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_mover_or_null() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) parse_my_tag() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocator method) (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_BasicOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPalette method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.core.scoring.etable.EtableOptions method) (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidue method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector method) (pyrosetta.rosetta.core.select.movemap.MoveMapFactory method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.ResnumFromStringsWithRangesSelector method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.chemistries.Chemistry method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) (pyrosetta.rosetta.protocols.chemistries.WrappedBaseChemistry method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) (pyrosetta.rosetta.protocols.denovo_design.architects.StructureArchitect method) (pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder method) (pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.connection.ConnectionArchitect method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures method) (pyrosetta.rosetta.protocols.features.DdGFeatures method) (pyrosetta.rosetta.protocols.features.FeaturesReporter method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures method) (pyrosetta.rosetta.protocols.features.HBondFeatures method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures method) (pyrosetta.rosetta.protocols.features.JobDataFeatures method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures method) (pyrosetta.rosetta.protocols.features.ModelFeatures method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures method) (pyrosetta.rosetta.protocols.features.PairFeatures method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures method) (pyrosetta.rosetta.protocols.features.ResidueFeatures method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures method) (pyrosetta.rosetta.protocols.features.RotamerFeatures method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures method) (pyrosetta.rosetta.protocols.features.SmotifFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) (pyrosetta.rosetta.protocols.features.StructureFeatures method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.MatchResidues method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover 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.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelector method) (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase 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.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirement method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirement method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandArea method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover 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.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck1B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheck2B method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.RamaCheckBase method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC 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.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefiner method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefiner method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetric method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_metric_calculators.FragQualCalculator method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector method) (pyrosetta.rosetta.protocols.pose_selectors.Filter method) (pyrosetta.rosetta.protocols.pose_selectors.LogicalSelector method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ConstantScoreBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridBase method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SingleGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporter method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelector method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) (pyrosetta.rosetta.protocols.simple_filters.AbinitioBaseFilter method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter method) (pyrosetta.rosetta.protocols.simple_filters.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.RGFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.SheetFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseBasicModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.options.StepWiseBasicOptions method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) parse_named_movemap_factory_legacy() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parse_NMR_name() (in module pyrosetta.rosetta.core.scoring.constraints) parse_optional_grid_set_from_tag() (in module pyrosetta.rosetta.protocols.qsar.scoring_grid) parse_options() (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.protocols.antibody.CDRSetOptionsParser method) (pyrosetta.rosetta.protocols.antibody.design.CDRGraftDesignOptionsParser method) (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptionsParser method) parse_opts() (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) parse_or_properties() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) parse_orientations() (in module pyrosetta.rosetta.protocols.denovo_design.components) parse_out_non_standard_residues() (in module pyrosetta.rosetta.core.sequence) parse_pdb_code() (in module pyrosetta.rosetta.protocols.splice) parse_pdb_file() (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) parse_pdbinfo_labels() (pyrosetta.rosetta.core.pose.PDBInfo method) parse_PDBnum_icode() (in module pyrosetta.rosetta.core.pose) parse_per_residue_tag() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) parse_plain_text_with_columns() (in module pyrosetta.rosetta.protocols.antibody.grafting) parse_profile_from_pose() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) parse_protocol_id_tag_item() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) parse_protocol_tag() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) parse_quota_command_line() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) parse_rama_map_file_shapovalov() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) parse_range() (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) parse_region_string() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) parse_relevant_residues_mode_tag_item() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) parse_remove_xray_virt_tag_item() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) parse_report_format_string() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter static method) parse_requirements() (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) parse_res_agnostic_commands() (in module pyrosetta.rosetta.core.pack.task) parse_resfile() (in module pyrosetta.rosetta.core.pack.task) parse_resfile_string() (in module pyrosetta.rosetta.core.pack.task) parse_resfile_string_with_no_lockdown() (in module pyrosetta.rosetta.protocols.forge.methods) parse_resfiles() (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) parse_residue() (pyrosetta.rosetta.core.scoring.constraints.ConstraintIO static method) parse_residue_level_task_operations() (in module pyrosetta.rosetta.core.pack.task.operation) parse_residue_selector() (in module pyrosetta.rosetta.core.select.residue_selector) parse_residue_selector_logic_string() (in module pyrosetta.rosetta.core.select.residue_selector) parse_resnames() (in module pyrosetta.rosetta.protocols.helical_bundle) parse_resnum() (in module pyrosetta.rosetta.core.pose) parse_resources_tag() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) parse_rotamer_sampling_data() (in module pyrosetta.rosetta.core.pack.task.operation) parse_schfile() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) parse_score_function() (in module pyrosetta.rosetta.core.scoring) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) parse_seeds() (in module pyrosetta.rosetta.protocols.seeded_abinitio) parse_segment_names() (in module pyrosetta.rosetta.protocols.denovo_design.connection) parse_segments() (pyrosetta.rosetta.protocols.splice.SpliceManager method) parse_sequence() (in module pyrosetta.rosetta.core.pose) parse_setting() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) parse_single_residue_selector() (in module pyrosetta.rosetta.protocols.jd3) parse_SpliceOut_tags() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) parse_startfrom_file() (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) parse_stride_tag_item() (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) parse_string_to_boolean_expression() (in module pyrosetta.rosetta.numeric.expression_parser) parse_string_to_expression() (in module pyrosetta.rosetta.numeric.expression_parser) parse_string_to_residue_selector() (pyrosetta.rosetta.core.select.residue_selector.SelectorLogicParser method) parse_stub_sets() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) parse_subtag() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) parse_tag() (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilter method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilter method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.ChainIs method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilter method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ReplicateTask method) (pyrosetta.rosetta.core.pack.task.operation.ResFilter method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterComposition method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabel method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabel method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilter method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAAS method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperation method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplings method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinks method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealer method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplings method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hotspot_hashing.AddSearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack1 method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack2 method) (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB method) (pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinCore method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) parse_tags() (pyrosetta.rosetta.protocols.splice.SpliceManager method) parse_target_tag() (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) parse_task_operations() (in module pyrosetta.rosetta.core.pack.task) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) parse_torsion_type() (in module pyrosetta.rosetta.protocols.constraint_generator) parse_use_transactions_tag_item() (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) parse_xyz_vector() (in module pyrosetta.rosetta.protocols.rosetta_scripts) parsed_string_for_resfile (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) ParsedProtocol (class in pyrosetta.rosetta.protocols.rosetta_scripts) ParsedProtocol.FilterReportTime (class in pyrosetta.rosetta.protocols.rosetta_scripts) ParsedProtocol.ParsedProtocolStep (class in pyrosetta.rosetta.protocols.rosetta_scripts) ParsedProtocolCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) ParsedTagCache (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) ParserJobInputter (class in pyrosetta.rosetta.protocols.protein_interface_design) ParserJobInputterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design) partial() (pyrosetta.rosetta.core.id.PartialAtomID method) partial_align() (in module pyrosetta.rosetta.protocols.hybridization) partial_assign_relaxed_state() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) partial_assign_state() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) partial_assign_state_with_lowest_one_body_energy() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) partial_charge() (pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom method) PartialAtomID (class in pyrosetta.rosetta.core.id) partially_assign_state() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) partially_solvated() (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityCalculator method) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityCalculator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) partialrms() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) PartialSecondarySimilarity (class in pyrosetta.rosetta.protocols.frag_picker.scores) PartialThreadingMover (class in pyrosetta.rosetta.protocols.comparative_modeling) Particle (class in pyrosetta.rosetta.core.optimization) ParticleSwarmMinimizer (class in pyrosetta.rosetta.core.optimization) partition_by_jump() (pyrosetta.rosetta.core.kinematics.FoldTree method) partition_by_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) partition_by_symm_jumps() (in module pyrosetta.rosetta.core.pose.symmetry) partition_coloring() (pyrosetta.rosetta.core.kinematics.FoldTree method) PARTITION_CONTACT (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) partition_definition() (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) partition_pose_by_jump() (in module pyrosetta.rosetta.core.pose) PartitionAggregateFunction (class in pyrosetta.rosetta.protocols.multistate_design) PartitionContactScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) PartitionedSearchPattern (class in pyrosetta.rosetta.protocols.hotspot_hashing) Partner (class in pyrosetta.rosetta.protocols.rigid) partner() (pyrosetta.rosetta.protocols.docking.DockingEnsemble method) partner1() (pyrosetta.rosetta.protocols.contact_map.Contact method) partner2() (pyrosetta.rosetta.protocols.contact_map.Contact method) partner_contact (pyrosetta.rosetta.protocols.sewing.data_storage.ContactDescription property) partner_downstream (pyrosetta.rosetta.protocols.rigid.Partner attribute) partner_ligand (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) partner_upstream (pyrosetta.rosetta.protocols.rigid.Partner attribute) PartnerMotifScorer (class in pyrosetta.rosetta.protocols.sewing.scoring) PartnerMotifScorerCreator (class in pyrosetta.rosetta.protocols.sewing.scoring) partners() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) pass_base_centroid_screen (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) pass_count() (pyrosetta.rosetta.protocols.stepwise.screener.AlignRMSD_Screener method) pass_metropolis() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SimAnnealerBase method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.flexpack.annealer.FlexbbSimAnnealer method) pass_start_pose() (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) pass_the_loop() (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) passed_automorphism() (pyrosetta.rosetta.protocols.motifs.MotifHit method) passes_com_vector_criterion() (pyrosetta.rosetta.protocols.match.NumNeighborsMPM method) passes_filter() (pyrosetta.rosetta.protocols.match.output.LimitHitsPerRotamerFilter method) (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.MatchFilter method) (pyrosetta.rosetta.protocols.match.output.StateAccumulatingMatchFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) passes_filters() (in module pyrosetta.rosetta.protocols.ligand_docking) passes_hardsphere_filter() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) passport() (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) passport_updated() (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) Patch (class in pyrosetta.rosetta.core.chemical) patch_file() (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) patch_map() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) patch_name (pyrosetta.rosetta.core.chemical.carbohydrates.SugarModificationsNomenclatureTableRow property) patch_name() (pyrosetta.rosetta.protocols.chemistries.PatchChemistry method) patch_name_from_affix() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager static method) patch_names() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) patch_str() (pyrosetta.rosetta.core.sequence.AnnotatedSequence method) PatchCase (class in pyrosetta.rosetta.core.chemical) PatchChemistry (class in pyrosetta.rosetta.protocols.chemistries) PatchChemistryCreator (class in pyrosetta.rosetta.protocols.chemistries) patchdock_entry_num() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) patchdock_fname() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) PatchdockReader (class in pyrosetta.rosetta.protocols.protein_interface_design) PatchdockTransform (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PatchdockTransformCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) patched_name() (pyrosetta.rosetta.core.chemical.Patch method) patches() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) PatchOperation (class in pyrosetta.rosetta.core.chemical) PatchOperationCreator (class in pyrosetta.rosetta.core.chemical) PatchOperationFactory (class in pyrosetta.rosetta.core.chemical) path() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) path_basename() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) path_dist() (pyrosetta.rosetta.core.scoring.AtomNeighbor method) (pyrosetta.rosetta.core.scoring.SmallAtNb method) path_distance() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.scoring.etable.count_pair.CountPairGeneric method) path_distances() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) PATH_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) path_tightness() (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) path_to_model (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionTensorflowProtocol property) path_to_scores_file_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) PATH_VECTOR_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) PathName (class in pyrosetta.rosetta.utility.file) pathname() (in module pyrosetta.rosetta.utility) PathOption (class in pyrosetta.rosetta.utility.options) PathOptionKey (class in pyrosetta.rosetta.utility.options) PathVectorOption (class in pyrosetta.rosetta.utility.options) PathVectorOptionKey (class in pyrosetta.rosetta.utility.options) patterson_corr_energy (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) PausableSignalHub_void_core_conformation_signals_GeneralEvent_t (class in pyrosetta.rosetta.utility.signals) pause() (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) pausing() (pyrosetta.rosetta.utility.signals.PausableSignalHub_void_core_conformation_signals_GeneralEvent_t method) Pb (pyrosetta.rosetta.core.chemical.element.Elements attribute) pb_bound_tag() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) PB_elec (pyrosetta.rosetta.core.scoring.ScoreType attribute) PB_elec_lr (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) PB_LIFETIME_CACHE (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) pb_unbound_tag() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) pbase() (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) pbe_mode (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) pbest() (pyrosetta.rosetta.core.optimization.Particle method) PBLifetimeCache (class in pyrosetta.rosetta.core.energy_methods) PBP_clustering_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) PCA (class in pyrosetta.rosetta.protocols.evaluation) pci_cation_pi (pyrosetta.rosetta.core.scoring.ScoreType attribute) pci_hbond (pyrosetta.rosetta.core.scoring.ScoreType attribute) pci_pi_pi (pyrosetta.rosetta.core.scoring.ScoreType attribute) pci_salt_bridge (pyrosetta.rosetta.core.scoring.ScoreType attribute) PCluster (class in pyrosetta.rosetta.protocols.pockets) PCluster.Cxyz (class in pyrosetta.rosetta.protocols.pockets) PClusterSet (class in pyrosetta.rosetta.protocols.pockets) pconf_creation() (pyrosetta.rosetta.protocols.environment.Environment method) pconf_destruction() (pyrosetta.rosetta.protocols.environment.Environment method) pcs (pyrosetta.rosetta.core.scoring.ScoreType attribute) pcs2 (pyrosetta.rosetta.core.scoring.ScoreType attribute) PCS_data (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_data_from_pose() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) PCS_data_input (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_data_input_manager (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_data_input_manager_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_data_input_manager_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_data_input_manager_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_data_input_manager_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_data_input_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_data_input_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_data_input_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_data_input_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_data_per_lanthanides (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_data_per_lanthanides_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_data_per_lanthanides_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_data_per_lanthanides_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_data_per_lanthanides_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_data_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_data_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_data_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_data_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_Energy (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_Energy_parameters_manager (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_Energy_parameters_manager_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_Energy_parameters_manager_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_Energy_parameters_manager_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_Energy_parameters_manager_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_Energy_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_Energy_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_Energy_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_Energy_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) pcs_erf() (in module pyrosetta.rosetta.core.scoring.nmr.pcs) PCS_experimental() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) PCS_file_data (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_file_data_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_file_data_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_file_data_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_file_data_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_FragDistance (class in pyrosetta.rosetta.protocols.frag_picker.scores) pcs_func() (in module pyrosetta.rosetta.core.scoring.nmr) PCS_line_data (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_line_data_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_line_data_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_line_data_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_line_data_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) pcs_lmmin() (in module pyrosetta.rosetta.protocols.nmr.pcs) PCS_multi_data_from_noone() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) PCS_multi_data_from_pose() (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) PCS_tensor (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PCS_tensor_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PCS_tensor_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PCS_tensor_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PCS_tensor_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) PCS_tolerance() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_line_data method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_line_data_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_line_data_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_line_data_Ts4 method) pcs_weight_stage1_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) pcs_weight_stage2_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) pcs_weight_stage3_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) pcs_weight_stage4_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) PCSData (class in pyrosetta.rosetta.core.scoring.nmr.pcs) PcsDataCenter (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsDataCenterManager (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsDataCenterManagerSingleton (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsDataLanthanide (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PCSEnergy (class in pyrosetta.rosetta.protocols.nmr.pcs) PcsEnergy (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsEnergyController (class in pyrosetta.rosetta.protocols.topology_broker) PCSEnergyCreator (class in pyrosetta.rosetta.protocols.nmr.pcs) PcsEnergyCreator (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsEnergyParameter (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsEnergyParameterManager (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsGridSearchParameter (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsGridSearchParameterManager (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsInputCenter (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsInputCenterManager (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsInputFile (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PcsInputLine (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PCSLigandTransformMover (class in pyrosetta.rosetta.protocols.nmr.pcs) PCSLigandTransformMoverCreator (class in pyrosetta.rosetta.protocols.nmr.pcs) PCSMultiGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) PCSMultiGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) PCSMultiSet (class in pyrosetta.rosetta.core.scoring.nmr.pcs) PCSSingle (class in pyrosetta.rosetta.core.scoring.nmr.pcs) PCSSingleGrid (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) PCSSingleGridCreator (class in pyrosetta.rosetta.protocols.qsar.scoring_grid) PCSSingleSet (class in pyrosetta.rosetta.core.scoring.nmr.pcs) PCSSingleSet.COMPUTATION_TYPE (class in pyrosetta.rosetta.core.scoring.nmr.pcs) PCSTensor (class in pyrosetta.rosetta.core.scoring.nmr.pcs) PcsTensor (class in pyrosetta.rosetta.protocols.scoring.methods.pcs2) PCSTensorOptimizer (class in pyrosetta.rosetta.protocols.nmr.pcs) pcsTs1 (pyrosetta.rosetta.core.scoring.ScoreType attribute) pcsTs2 (pyrosetta.rosetta.core.scoring.ScoreType attribute) pcsTs3 (pyrosetta.rosetta.core.scoring.ScoreType attribute) pcsTs4 (pyrosetta.rosetta.core.scoring.ScoreType attribute) Pd (pyrosetta.rosetta.core.chemical.element.Elements attribute) pd_ (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator property) pd_reader() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform method) pdamp() (pyrosetta.rosetta.core.scoring.MultipoleParameter method) PDatom (class in pyrosetta.rosetta.core.scoring) PDB (class in pyrosetta.rosetta.protocols.sparta) pdb (pyrosetta.rosetta.protocols.antibody.CDRDBPose property) (pyrosetta.rosetta.protocols.antibody.CDRDBSequence property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) pdb() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) pdb2pose() (pyrosetta.rosetta.core.pose.PDBInfo method) pdb_author() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) pdb_chain() (pyrosetta.rosetta.protocols.pmut_scan.MutationData method) pdb_code_ (pyrosetta.rosetta.protocols.legacy_sewing.Model property) pdb_code_from_rosetta_name() (pyrosetta.rosetta.core.io.NomenclatureManager static method) pdb_comments (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) pdb_comments() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) pdb_conformers (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) pdb_conformers_string (pyrosetta.rosetta.protocols.sewing.data_storage.LigandDescription property) pdb_count() (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) PDB_DIR (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) pdb_end() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) PDB_Entry (class in pyrosetta.rosetta.protocols.sparta) PDB_file (pyrosetta.rosetta.core.import_pose.FileType attribute) PDB_FILE (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) PDB_FORMAT (pyrosetta.rosetta.utility.DateFormat attribute) pdb_id (pyrosetta.rosetta.protocols.loophash.BBExtraData property) pdb_info (pyrosetta.bindings.pose.ResidueLabelAccessor attribute) pdb_info() (pyrosetta.rosetta.core.pose.Pose method) PDB_LIST (pyrosetta.rosetta.protocols.cluster.calibur.INPUT_FILE_TYPE attribute) pdb_name() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) pdb_name_ (pyrosetta.rosetta.protocols.pack_daemon.StructureFileNames property) pdb_num (pyrosetta.rosetta.core.io.raw_data.DisulfideFile attribute) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile.NumberingSystem attribute) pdb_numb() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) pdb_numbering() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) pdb_output() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) pdb_parents() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) pdb_position_ (pyrosetta.rosetta.protocols.antibody.design.MutantPosition property) pdb_prefix() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) pdb_profile() (pyrosetta.rosetta.protocols.splice.RotLibdb method) (pyrosetta.rosetta.protocols.splice.SpliceSegment method) pdb_rotamers_file() (pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification method) pdb_rsd() (in module pyrosetta.bindings.pose) (pyrosetta.rosetta.core.pose.Pose method) pdb_segments() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.BasisMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.EdgeMapGenerator method) (pyrosetta.rosetta.protocols.sewing.hashing.Hasher method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) pdb_start (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) pdb_start() (pyrosetta.rosetta.protocols.antibody.clusters.CDRCluster method) pdb_stop (pyrosetta.rosetta.protocols.forge.remodel.RemodelData property) pdb_to_next_allowed_partners() (pyrosetta.rosetta.protocols.splice.BBMatching method) pdb_to_pose() (in module pyrosetta.rosetta.core.pose) pdb_to_prev_allowed_partners() (pyrosetta.rosetta.protocols.splice.BBMatching method) pdb_to_profile_map() (pyrosetta.rosetta.protocols.splice.SpliceSegment method) PDBChunkLibraryInputter (class in pyrosetta.rosetta.protocols.jd3.chunk_library_inputters) PDBChunkLibraryInputterCreator (class in pyrosetta.rosetta.protocols.jd3.chunk_library_inputters) PdbDataFeatures (class in pyrosetta.rosetta.protocols.features) PdbDataFeaturesCreator (class in pyrosetta.rosetta.protocols.features) PDBDumpMover (class in pyrosetta.rosetta.protocols.moves) PDBfileName (pyrosetta.rosetta.protocols.sparta.PDB property) PDBFullModelInputter (class in pyrosetta.rosetta.protocols.jd3.full_model_inputters) PDBFullModelInputterCreator (class in pyrosetta.rosetta.protocols.jd3.full_model_inputters) pdbid() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) PdbIdChunkFilter (class in pyrosetta.rosetta.protocols.frag_picker) PDBInfo (class in pyrosetta.rosetta.core.pose) PDBInfo.AtomRecord (class in pyrosetta.rosetta.core.pose) PDBInfo.ResidueRecord (class in pyrosetta.rosetta.core.pose) PDBJobInputter (class in pyrosetta.rosetta.protocols.jd2) PDBJobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) PDBJobOutputter (class in pyrosetta.rosetta.protocols.jd2) PDBJobOutputterCreator (class in pyrosetta.rosetta.protocols.jd2) PDBLandmark (class in pyrosetta.rosetta.protocols.antibody) pdbListName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) pdbn (pyrosetta.rosetta.protocols.constel.ResMut property) pdbname() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) PDBNumbering (class in pyrosetta.rosetta.protocols.antibody.design) PDBOutput (class in pyrosetta.rosetta.protocols.dna) pdboutput() (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) pdbpos (pyrosetta.rosetta.protocols.dna.DnaDesignDef property) pdbpos() (pyrosetta.rosetta.core.fragment.AnnotatedFragData method) (pyrosetta.rosetta.core.fragment.FragData method) PDBPoseInputStream (class in pyrosetta.rosetta.core.import_pose.pose_stream) PDBPoseInputter (class in pyrosetta.rosetta.protocols.jd3.pose_inputters) PDBPoseInputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_inputters) PDBPoseMap (class in pyrosetta.rosetta.core.pose) PDBPoseOutputSpecification (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) PDBPoseOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) PDBPoseOutputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) PDBReloadMover (class in pyrosetta.rosetta.protocols.simple_moves) PDBReloadMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) PDBRotamerLibrarySpecification (class in pyrosetta.rosetta.core.chemical.rotamers) PDBRotamerLibrarySpecificationCreator (class in pyrosetta.rosetta.core.chemical.rotamers) PDBs_ (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) PDBSilentStruct (class in pyrosetta.rosetta.core.import_pose) PDBSilentStructCreator (class in pyrosetta.rosetta.core.import_pose) pdbslice() (in module pyrosetta.rosetta.core.pose) (in module pyrosetta.rosetta.protocols.magnesium) PDBTrajectoryRecorder (class in pyrosetta.rosetta.protocols.canonical_sampling) PDBTrajectoryRecorderCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) PDBWriter (class in pyrosetta.rosetta.protocols.match.output) pddf_score (pyrosetta.rosetta.core.scoring.ScoreType attribute) PDDFEnergy (class in pyrosetta.rosetta.protocols.scoring.methods.saxs) PDDFEnergyCreator (class in pyrosetta.rosetta.protocols.scoring.methods.saxs) PDDFScoreFilter (class in pyrosetta.rosetta.protocols.simple_filters) PDEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) pdie (pyrosetta.rosetta.core.scoring.APBSConfig.R_PARAM property) PDinter (class in pyrosetta.rosetta.core.scoring) (class in pyrosetta.rosetta.core.scoring.power_diagram) PDInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) PDNode (class in pyrosetta.rosetta.core.pack.interaction_graph) PDsphere (class in pyrosetta.rosetta.core.scoring.power_diagram) PDvertex (class in pyrosetta.rosetta.core.scoring) (class in pyrosetta.rosetta.core.scoring.power_diagram) peak_id() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) peak_volume() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) PeakAssignment (class in pyrosetta.rosetta.protocols.noesy_assign) PeakAssignmentParameters (class in pyrosetta.rosetta.protocols.noesy_assign) PeakAssignmentResidueMap (class in pyrosetta.rosetta.protocols.noesy_assign) PeakCalibrator (class in pyrosetta.rosetta.protocols.noesy_assign) PeakCalibratorMap (class in pyrosetta.rosetta.protocols.noesy_assign) PeakFileFormat (class in pyrosetta.rosetta.protocols.noesy_assign) PeakFileFormat_Base (class in pyrosetta.rosetta.protocols.noesy_assign) PeakFileFormat_Sparky (class in pyrosetta.rosetta.protocols.noesy_assign) PeakFileFormat_xeasy (class in pyrosetta.rosetta.protocols.noesy_assign) PeakFileFormat_xpk (class in pyrosetta.rosetta.protocols.noesy_assign) peaks() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) peek() (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wistream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) peek_back() (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareByScoreCombination_t method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) peek_front() (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareByScoreCombination_t method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) penalty() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.scoring.MembraneEmbed method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeEnergySetup method) penalty_per_sap() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) penalty_per_unit() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) penalty_wtd_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) PENTOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) pep1 (pyrosetta.rosetta.core.io.CisPeptideInformation property) pep2 (pyrosetta.rosetta.core.io.CisPeptideInformation property) pep_fold_only (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) pep_refine (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) pep_start (pyrosetta.rosetta.protocols.peptide_deriver.DerivedPeptideEntry property) PEPTIDE (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibPolymerType attribute) peptide_anchors (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) peptide_bond (pyrosetta.rosetta.core.scoring.ScoreType attribute) peptide_chain() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) peptide_cuts (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) peptide_entry() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) peptide_first_res() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) peptide_last_res() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) peptide_length() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) peptide_loop_model (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) peptide_nres() (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags method) peptide_stub_mover_initialized() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) PeptideBondEnergy (class in pyrosetta.rosetta.core.energy_methods) PeptideBondEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) PeptideCyclizeMover (class in pyrosetta.rosetta.protocols.cyclic_peptide) PeptideCyclizeMoverCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) PeptideDeriverBasicStreamOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverEntryType (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverFilter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverFilterCreator (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverMarkdownStreamOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverOutputterContainer (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverPoseOutputter (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideDeriverReportFormat (class in pyrosetta.rosetta.protocols.peptide_deriver) PeptideInternalHbondsFilter (class in pyrosetta.rosetta.protocols.cyclic_peptide) PeptideInternalHbondsFilterCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) PeptideInternalHbondsMetric (class in pyrosetta.rosetta.protocols.cyclic_peptide) PeptideInternalHbondsMetricCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) PeptideOrientationMover (class in pyrosetta.rosetta.protocols.membrane_benchmark) PeptideOrientationMoverCreator (class in pyrosetta.rosetta.protocols.membrane_benchmark) PeptideStapleDesignMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PeptideStapleDesignMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PeptideStapleMover (class in pyrosetta.rosetta.protocols.simple_moves) PeptideStubMover (class in pyrosetta.rosetta.protocols.cyclic_peptide) PeptideStubMoverCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) PeptideTorsionReporter (class in pyrosetta.rosetta.core.pack.dunbrack) PEPTOID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibPolymerType attribute) PeptoidGeneralDOFReporter (class in pyrosetta.rosetta.core.pack.dunbrack) PeptoidOmegaReporter (class in pyrosetta.rosetta.core.pack.dunbrack) per_atom_lipid_accessibility() (pyrosetta.rosetta.core.conformation.membrane.MembraneInfo method) per_chain_renumbering() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) per_res_lddt() (in module pyrosetta.rosetta.core.scoring) per_res_rms_at_corresponding_atoms_no_super() (in module pyrosetta.rosetta.core.scoring) per_res_sc_sasa() (in module pyrosetta.rosetta.core.scoring.sasa) per_residue_probabilities_data_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) per_residue_probabilities_output_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) per_residue_real_data_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) per_residue_real_output_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) per_residue_string_data_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) per_residue_string_output_ (pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct property) PERCENT_EDGES (pyrosetta.rosetta.protocols.cluster.calibur.EST_THRESHOLD_MODE attribute) percent_hbond_capacity (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) percent_native() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) perform_ABOXYZ_bin_analysis_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) perform_all_reactions() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) perform_major_reaction_only() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) perform_validation_test() (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) performing_pure_insertion() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) performs_major_reaction_only() (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) period() (pyrosetta.rosetta.core.scoring.methods.BBDepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.BBIndepCartBondedParameters method) (pyrosetta.rosetta.core.scoring.methods.CartBondedParameters method) PERIODIC (pyrosetta.rosetta.numeric.interpolation.CatmullRomSplineBoundaryType attribute) periodic_mod() (pyrosetta.rosetta.core.scoring.electron_density.ElectronDensity method) periodic_range() (in module pyrosetta.rosetta.basic) PeriodicBoundFunc (class in pyrosetta.rosetta.core.scoring.constraints) PeriodicBoxMover (class in pyrosetta.rosetta.protocols.simple_moves) PeriodicBoxMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) PeriodicFunc (class in pyrosetta.rosetta.core.scoring.func) periodicity() (pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) permitted_overlap() (pyrosetta.rosetta.protocols.match.MatcherTask method) permutate_n_vv_of_pairs() (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) permutation_setting() (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) Permute (class in pyrosetta.rosetta.basic.sampling.orientations) PerNativeRRReporterHuman (class in pyrosetta.rosetta.protocols.rotamer_recovery) PerResidueClashMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueClashMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueDensityFitMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueDensityFitMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueEnergyMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueEnergyMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueEsmProbabilitiesMetric (class in pyrosetta.rosetta.protocols.esm_perplexity) PerResidueEsmProbabilitiesMetricCreator (class in pyrosetta.rosetta.protocols.esm_perplexity) PerResidueGlycanLayerMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueGlycanLayerMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueInterfaceData (class in pyrosetta.rosetta.protocols.analysis) PerResidueProbabilitiesMetric (class in pyrosetta.rosetta.core.simple_metrics) PerResidueRealMetric (class in pyrosetta.rosetta.core.simple_metrics) PerResidueRMSDMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueRMSDMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueSapScoreMetric (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) PerResidueSapScoreMetricCreator (class in pyrosetta.rosetta.core.pack.guidance_scoreterms.sap) PerResidueSasaMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueSasaMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) PerResidueStringMetric (class in pyrosetta.rosetta.core.simple_metrics) PerSphereAccumulator (class in pyrosetta.rosetta.core.scoring.packstat) pert() (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) pert_size() (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) PertMinMover (class in pyrosetta.rosetta.protocols.minimization_packing) PertMinMoverCreator (class in pyrosetta.rosetta.protocols.minimization_packing) perturb (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GenKICPerturberEffect attribute) perturb() (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) perturb_anchor() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) perturb_angles() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_backbone_by_bins (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) perturb_backbone_for_test() (in module pyrosetta.rosetta.protocols.grafting) perturb_beta_residue() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.TorsionSamplingKinematicPerturber method) perturb_bondangle (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) perturb_bondlength (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) perturb_c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_c_n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_ca_c_n() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_chain() (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) perturb_chis() (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) perturb_dBR_and_relax() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) perturb_dihedral (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) perturb_dihedral_bbg (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect attribute) perturb_lattice() (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) perturb_lengths() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_ligand_rb() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) perturb_ligand_torsions() (in module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) perturb_molecule_move() (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) perturb_n_ca() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_n_ca_c() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_omega() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_phi() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_psi() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_rb (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions property) perturb_rb() (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) perturb_rb_rotation (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions property) perturb_rb_translation (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions property) perturb_sBR_and_relax() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) perturb_sequence() (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_subset() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_subset_with_balance() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturb_torsion (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions property) perturb_torsion_rotation (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions property) perturb_torsions() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) perturb_weights() (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) perturb_with_balance() (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.BondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.FragmentPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.IdealizeNonPhiPsi method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.LogFilePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.OmegaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Perturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.PerturberSet method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.Rama2bPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.RamaPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.UniformPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.VicinityPerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingBondAnglePerturber method) (pyrosetta.rosetta.protocols.kinematic_closure.perturbers.WalkingPerturber method) (pyrosetta.rosetta.protocols.loop_modeler.perturbers.LoopHashPerturber method) perturbation_magnitude() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) perturbation_set() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) perturbation_type() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) perturbation_type_enum_from_string() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter static method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter static method) perturbation_type_string_from_enum() (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter static method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter static method) PerturbBundle (class in pyrosetta.rosetta.protocols.helical_bundle) PerturbBundleCreator (class in pyrosetta.rosetta.protocols.helical_bundle) PerturbBundleHelix (class in pyrosetta.rosetta.protocols.helical_bundle) PerturbBundleHelixCreator (class in pyrosetta.rosetta.protocols.helical_bundle) PerturbByBins (class in pyrosetta.rosetta.protocols.simple_moves.bin_transitions) PerturbByBinsCreator (class in pyrosetta.rosetta.protocols.simple_moves.bin_transitions) PerturbChiSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) PerturbChiSidechainMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) perturbed_sequence() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) Perturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) perturber() (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) perturber_effect (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber) perturber_exhausted() (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) perturber_type() (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) PerturberSet (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) PerturbRotamerSidechainMover (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) PerturbRotamerSidechainMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves.sidechain_moves) perturbtorsion_gaussian (pyrosetta.rosetta.protocols.simple_moves.TorsionPerturbType attribute) perturbtorsion_uniform (pyrosetta.rosetta.protocols.simple_moves.TorsionPerturbType attribute) perturbtorsion_unknown (pyrosetta.rosetta.protocols.simple_moves.TorsionPerturbType attribute) PG_like (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) pH_MODE_EXCEPTIONS (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) pH_mode_exceptions() (in module pyrosetta.rosetta.core.chemical) PH_PO (pyrosetta.rosetta.core.scoring.motif.RPM_Type attribute) Pharmacophore (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) pharmacophores_defined() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) phase() (pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent method) pHEnergy (class in pyrosetta.rosetta.core.energy_methods) pHEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) PhenixInterface (class in pyrosetta.rosetta.core.scoring.cryst) Phi (class in pyrosetta.rosetta.protocols.frag_picker.scores) PHI (pyrosetta.rosetta.core.chemical.rings.CPParameter attribute) phi (pyrosetta.rosetta.core.fragment.torsions property) PHI (pyrosetta.rosetta.core.id.DOF_Type attribute) (pyrosetta.rosetta.core.scoring.ProteinTorsion attribute) phi (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueBackboneEntry property) (pyrosetta.rosetta.protocols.jumping.DisulfTemplate property) (pyrosetta.rosetta.protocols.jumping.PairingTemplate property) (pyrosetta.rosetta.protocols.pockets.spherical_coor_triplet property) (pyrosetta.rosetta.protocols.pockets.triplet_and_originnum property) phi() (pyrosetta.rosetta.core.chemical.Adduct method) (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.chemical.MutableICoorRecord method) (pyrosetta.rosetta.core.chemical.orbitals.ICoorOrbitalData method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.motif.Xfres method) (pyrosetta.rosetta.core.scoring.power_diagram.SAnode method) (pyrosetta.rosetta.core.scoring.SAnode method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairing method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.splice.BBDofs method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) phi_ (pyrosetta.rosetta.protocols.loop_grower.ResTorsions property) PHI_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) phi_dihedral (pyrosetta.rosetta.core.id.MainchainTorsionType attribute) phi_index() (pyrosetta.rosetta.core.scoring.OmegaTether method) phi_max() (pyrosetta.rosetta.core.sequence.ABEGO method) phi_min() (pyrosetta.rosetta.core.sequence.ABEGO method) phipsi_in_allowed_rama() (pyrosetta.rosetta.core.scoring.Ramachandran method) phipsi_in_forbidden_rama() (pyrosetta.rosetta.core.scoring.Ramachandran method) PhiPsiRmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) PhiPsiSquareWell (class in pyrosetta.rosetta.protocols.frag_picker.scores) PhiPsiTalosIO (class in pyrosetta.rosetta.protocols.frag_picker) phis (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData property) PhiSelector (class in pyrosetta.rosetta.core.select.residue_selector) PhiSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) phores() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) PHOSPHATE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.chemical.rna.BaseEdge attribute) (pyrosetta.rosetta.RNAAtomType attribute) phosphate_base_phosphate_rmsd() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) phosphate_base_phosphate_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) phosphate_move_list() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) PHOSPHATE_PACK (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) phosphate_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) PhosphateMove (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) PhosphateMover (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) PhosphateScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) PhosphateTerminus (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) PHOSPHONATE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PHOSPHONATE_UPPER (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PHOSPHONATE_UPPER_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) PHOSPHORYLATED_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PHOSPHORYLATION (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric.PTMPredictionMetricModes attribute) pHVariantTaskOperation (class in pyrosetta.rosetta.protocols.task_operations) pHVariantTaskOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) physical() (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) pi() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) pi_2() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) pi_2_over_3() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) pi_3_over_4() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) PI_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) pi_over_180() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) pi_over_2() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) pi_over_3() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) pi_over_4() (pyrosetta.rosetta.numeric.NumericTraits_double_t static method) (pyrosetta.rosetta.numeric.NumericTraits_float_t static method) (pyrosetta.rosetta.numeric.NumericTraits_long_double_t static method) pick() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.GapSolutionPicker method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers.RandomGapSolutionPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.EndToEndPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedOffsetsPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.FixedPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.LoopPivots method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.PivotPicker method) (pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers.StandardPivots method) pick_a_rotamer() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) pick_a_rotamer_for_node() (pyrosetta.rosetta.core.pack.annealer.DebuggingAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FASTERAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbCoupledRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbLinkingRotamerSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbPwatSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.FixbbSimAnnealer method) (pyrosetta.rosetta.core.pack.annealer.MultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.annealer.RotamerAssigningAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SequenceSymmetricAnnealer method) (pyrosetta.rosetta.core.pack.annealer.SmartFixbbSimAnnealer method) pick_and_apply() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.RandomSolutions method) (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.SolutionPicker method) pick_and_cache_fragments() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) pick_baserotamer_from_rotblock() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet method) pick_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) pick_chunk_candidates() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) pick_consensus_AA() (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) pick_consensus_AA_mpi() (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) pick_fragments() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) pick_fragments_by_ss() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) pick_fragments_by_ss_plus_aa() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) pick_fragments_public() (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) pick_frags() (pyrosetta.rosetta.protocols.abinitio.Templates method) pick_large_frags() (pyrosetta.rosetta.protocols.abinitio.Template method) (pyrosetta.rosetta.protocols.abinitio.Templates method) pick_loops_chainbreak() (in module pyrosetta.rosetta.protocols.loops) pick_loops_unaligned() (in module pyrosetta.rosetta.protocols.loops) pick_loopy_cutpoint() (in module pyrosetta.rosetta.core.kinematics) pick_new_cutpoints() (pyrosetta.rosetta.protocols.anchored_design.AnchorMoversData method) pick_objfunction() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) pick_random_chunk() (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) pick_random_starting_segment() (pyrosetta.rosetta.protocols.sewing.data_storage.HashedSmartAssembly method) (pyrosetta.rosetta.protocols.sewing.data_storage.SmartAssembly method) pick_random_template() (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) pick_sequence_from_database() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) pick_solution() (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover static method) pick_starting_template() (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) pick_strategy() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) Picker (class in pyrosetta.rosetta.protocols.denovo_design.components) picking_rounds() (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) pickled_pose (pyrosetta.distributed.packed_pose.core.PackedPose attribute) PickRandomSegmentMover (class in pyrosetta.rosetta.protocols.pose_sewing.movers) PickRandomSegmentMoverCreator (class in pyrosetta.rosetta.protocols.pose_sewing.movers) pieces() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub method) PIKAA (class in pyrosetta.rosetta.core.pack.task) PIKNA (class in pyrosetta.rosetta.core.pack.task) PiOrbitalElectronegativityMulliken (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) PiOrbitalElectronegativityPauling (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) PiPiCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) PiValenceStateElectronAffinity (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) PiValenceStateIonizationPotential (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.Properties attribute) pivot() (pyrosetta.rosetta.numeric.MathMatrix_double_t method) (pyrosetta.rosetta.numeric.MathMatrix_float_t method) pivot1() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) pivot2() (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) pivot_atoms() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) pivot_loop() (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) pivot_residues() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) PivotPicker (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) place() (pyrosetta.rosetta.core.conformation.Residue method) place_atom() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) place_atom_() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) place_atom_positions() (in module pyrosetta.rosetta.protocols.helical_bundle) place_atoms() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) place_atoms_() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) place_c() (pyrosetta.rosetta.protocols.kinmatch.BruteFunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.FunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.KinFunGroupTK method) place_cut_site_in_segment() (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) place_d() (pyrosetta.rosetta.protocols.kinmatch.BruteFunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.FunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.KinFunGroupTK method) place_de_novo_wat_at_anchor() (in module pyrosetta.rosetta.protocols.hydrate) place_h() (pyrosetta.rosetta.protocols.kinmatch.BruteFunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.FunGroupTK method) (pyrosetta.rosetta.protocols.kinmatch.KinFunGroupTK method) place_near_origin() (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) place_new_restype_no_align() (in module pyrosetta.rosetta.protocols.drug_design) place_origin_point() (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) place_peptide (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) place_residue() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) place_residue_() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) place_rots_on_pose() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) place_sidechain_in_pose() (pyrosetta.rosetta.core.scoring.motif.Xfres method) place_stubs() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) place_VRT_at_residue_COM() (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) PlaceableRotamer (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) placeholder_clone() (pyrosetta.rosetta.core.chemical.MutableResidueType method) placeholder_info() (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) placeholder_info_ (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo property) placeholder_residue() (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) placeholder_residue_ (pyrosetta.rosetta.core.scoring.facts.FACTSPoseInfo property) PlacementAuctionMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlacementAuctionMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlacementMinimizationMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlacementMinimizationMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceOnLoop (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceOnLoopCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceProbeMover (class in pyrosetta.rosetta.protocols.hotspot_hashing.movers) PlaceProbeMover.ExecutionMode (class in pyrosetta.rosetta.protocols.hotspot_hashing.movers) PlaceProbeMover.StructureOutputMode (class in pyrosetta.rosetta.protocols.hotspot_hashing.movers) placeResidueAtTransform() (pyrosetta.rosetta.protocols.hotspot_hashing.StubGenerator static method) placeResidueOnPose() (pyrosetta.rosetta.protocols.hotspot_hashing.StubGenerator static method) PlaceSimultaneouslyMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceSimultaneouslyMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceStubMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceStubMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PlaceSurfaceProbe (class in pyrosetta.rosetta.protocols.hotspot_hashing.movers) PlaceSurfaceProbe.ExecutionMode (class in pyrosetta.rosetta.protocols.hotspot_hashing.movers) PlaceSurfaceProbe.StructureOutputMode (class in pyrosetta.rosetta.protocols.hotspot_hashing.movers) PlaceSurfaceProbeCreator (class in pyrosetta.rosetta.protocols.hotspot_hashing.movers) PlaidFingerprint (class in pyrosetta.rosetta.protocols.pockets) PlainPdbJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) PlainRawJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) PlainSilentFileJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) PLATFORM (pyrosetta.rosetta.core.scoring.rna.RNA_MotifType attribute) Pleating() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) pleats1() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) pleats2() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairing method) Ploop2x3 (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) Ploop3x3 (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) PLUS_SYMBOL (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) Pm (pyrosetta.rosetta.core.chemical.element.Elements attribute) pmatch() (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) pml_file_written (pyrosetta.rosetta.protocols.hbnet.HBondNetStruct property) pmut (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams property) PNA (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PNatAAOptEPositionData (class in pyrosetta.rosetta.protocols.optimize_weights) PNatAAOptERotamerData (class in pyrosetta.rosetta.protocols.optimize_weights) PNatLigPoseOptEData (class in pyrosetta.rosetta.protocols.optimize_weights) PNatRotOptEPositionData (class in pyrosetta.rosetta.protocols.optimize_weights) PNatRotOptERotamerData (class in pyrosetta.rosetta.protocols.optimize_weights) PNatStructureOptEData (class in pyrosetta.rosetta.protocols.optimize_weights) pnear() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_PNearToArbitraryStateSummary method) PNearCalculator (class in pyrosetta.rosetta.protocols.cyclic_peptide_predict) Po (pyrosetta.rosetta.core.chemical.element.Elements attribute) pocket_cc (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo property) pocket_CoM_ (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint property) pocket_constraint (pyrosetta.rosetta.core.scoring.ScoreType attribute) PocketConstraint (class in pyrosetta.rosetta.protocols.pockets) PocketConstraintCreator (class in pyrosetta.rosetta.protocols.pockets) PocketExemplarMultifunc (class in pyrosetta.rosetta.protocols.pockets) PocketGrid (class in pyrosetta.rosetta.protocols.pockets) pocketGrid_dim_ (pyrosetta.rosetta.protocols.pockets.FingerprintBase property) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint property) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint property) pocketGrid_mid_ (pyrosetta.rosetta.protocols.pockets.FingerprintBase property) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint property) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint property) pocketGrid_spacing_ (pyrosetta.rosetta.protocols.pockets.FingerprintBase property) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint property) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint property) Point (class in pyrosetta.rosetta.core.scoring.packstat) (class in pyrosetta.rosetta.numeric.interpolation.spline) (class in pyrosetta.rosetta.RDGeom) point (pyrosetta.rosetta.core.scoring.sc._PROBE property) point() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (pyrosetta.rosetta.numeric.kdtree.KDNode method) point3d (class in pyrosetta.rosetta.core.scoring.atomic_depth) Point3D (class in pyrosetta.rosetta.RDGeom) point_clash_energy() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) point_energy() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) point_for_nonchitip_atom() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) point_in_ellipse() (in module pyrosetta.rosetta.numeric.linear_algebra) point_inside() (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) point_on_ellipsoid() (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) point_radius_ (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) point_search_end_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) point_search_start_ (pyrosetta.rosetta.protocols.electron_density.DensityGridSearchOptions property) PointDwell (class in pyrosetta.rosetta.core.pack.annealer) PointGraphEdgeData (class in pyrosetta.rosetta.core.conformation) PointGraphPy (class in pyrosetta.rosetta.core.conformation) PointGraphVertexData (class in pyrosetta.rosetta.core.conformation) PointMutationCalculator (class in pyrosetta.rosetta.protocols.design_opt) PointMutScanDriver (class in pyrosetta.rosetta.protocols.pmut_scan) PointPair (class in pyrosetta.rosetta.core.scoring.packstat) points_ (pyrosetta.rosetta.protocols.pockets.CCluster property) (pyrosetta.rosetta.protocols.pockets.PCluster property) (pyrosetta.rosetta.protocols.sic_dock.CBScore property) points_for_nonchitip_atoms() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) points_in_triangle() (in module pyrosetta.rosetta.core.membrane) points_to_search() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) PointScoreComparator (class in pyrosetta.rosetta.protocols.electron_density) (class in pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock) pointwater (pyrosetta.rosetta.core.scoring.ScoreType attribute) PointWaterEnergy (class in pyrosetta.rosetta.core.energy_methods) PointWaterEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) PointWaterPotential (class in pyrosetta.rosetta.core.scoring) PoissonBoltzmannEnergy (class in pyrosetta.rosetta.core.energy_methods) PoissonBoltzmannEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) PoissonBoltzmannPotential (class in pyrosetta.rosetta.core.scoring) POLAR (class in pyrosetta.rosetta.core.pack.task) (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) POLAR_HYDROGEN (pyrosetta.rosetta.core.chemical.AtomProperty attribute) polar_max (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property) polar_min (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property) polar_rotation_sampling (pyrosetta.rosetta.protocols.hotspot_hashing.SphericalRotationSearchPattern property) POLAR_SASA (pyrosetta.rosetta.core.scoring.sasa.SasaMethodHPMode attribute) polar_sasa() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) polar_sc_atoms_not_satisfied_by_background() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) polar_scale() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) PolarGroupBurialPyMolStringMetric (class in pyrosetta.rosetta.protocols.analysis.burial_metrics) PolarGroupBurialPyMolStringMetricCreator (class in pyrosetta.rosetta.protocols.analysis.burial_metrics) polarH() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties method) PolarHydrogenFilter (class in pyrosetta.rosetta.core.chemical) PolarHydrogenPacker (class in pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens) polarity() (pyrosetta.rosetta.core.scoring.MultipoleParameter method) polarity_avg0 (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityResults property) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityResults property) polarity_avg1 (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityResults property) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityResults property) polarity_mag_avg0 (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityResults property) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityResults property) polarity_mag_avg1 (pyrosetta.rosetta.core.scoring.sc.ElectrostaticComplementarityResults property) (pyrosetta.rosetta.core.scoring.sc.ElectrostaticSimilarityResults property) poly_ala() (pyrosetta.rosetta.protocols.splice.Splice method) polycubic_interpolation() (in module pyrosetta.rosetta.core.pack.dunbrack) PolycubicSpline_1_t (class in pyrosetta.rosetta.numeric.interpolation.spline) PolycubicSpline_2_t (class in pyrosetta.rosetta.numeric.interpolation.spline) PolycubicSpline_3_t (class in pyrosetta.rosetta.numeric.interpolation.spline) PolycubicSpline_4_t (class in pyrosetta.rosetta.numeric.interpolation.spline) PolycubicSpline_5_t (class in pyrosetta.rosetta.numeric.interpolation.spline) PolycubicSpline_6_t (class in pyrosetta.rosetta.numeric.interpolation.spline) PolycubicSplineBase (class in pyrosetta.rosetta.numeric.interpolation.spline) POLYMER (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) polymer (pyrosetta.rosetta.protocols.sewing.data_storage.PolymericType attribute) polymer_direction() (pyrosetta.rosetta.core.kinematics.Edge method) POLYMER_LOWER (pyrosetta.rosetta.core.chemical.ICoordAtomIDType attribute) POLYMER_UPPER (pyrosetta.rosetta.core.chemical.ICoordAtomIDType attribute) PolymerBondedEnergyContainer (class in pyrosetta.rosetta.core.scoring) PolymerBondedNeighborConstIterator (class in pyrosetta.rosetta.core.scoring) PolymerBondedNeighborIterator (class in pyrosetta.rosetta.core.scoring) polymeric_oriented_sequence_distance() (pyrosetta.rosetta.core.conformation.Residue method) polymeric_sequence_distance() (pyrosetta.rosetta.core.conformation.Residue method) PolymericType (class in pyrosetta.rosetta.protocols.sewing.data_storage) polynom_by_z() (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) Polynomial_1d (class in pyrosetta.rosetta.core.scoring.hbonds) (class in pyrosetta.rosetta.numeric) pool (class in pyrosetta.rosetta.cppdb) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams property) pool_ (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.PoolData property) Pool_ConvergenceCheck (class in pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) Pool_Evaluator (class in pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) pool_exists() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) Pool_RMSD (class in pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) POOL_RMSD_ADD_STRUCTURE (pyrosetta.rosetta.basic.ProfTag attribute) POOL_RMSD_EVALUATE (pyrosetta.rosetta.basic.ProfTag attribute) POOL_RMSD_MASTER_EVALUATE (pyrosetta.rosetta.basic.ProfTag attribute) pool_size() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) PoolData (class in pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks) PoolEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) pop() (pyrosetta.bindings.pose.PoseScoreAccessor method) (pyrosetta.bindings.pose.ResidueLabelAccessor method) (pyrosetta.io.silent_file_map.SilentFileMap method) (pyrosetta.rosetta.core.fragment.FrameList method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.core.io.Remarks method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.numeric.expression_parser.TokenSet method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.pack_daemon.TopEntitySet method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) (pyrosetta.rosetta.std.priority_queue_protocols_motif_grafting_movers_MotifMatch_std_vector_protocols_motif_grafting_movers_MotifMatch_std_less_protocols_motif_grafting_movers_MotifMatch_t method) (pyrosetta.rosetta.std.vector_core_io_AtomInformation method) (pyrosetta.rosetta.std.vector_core_io_RemarkInfo method) (pyrosetta.rosetta.std.vector_core_pose_Pose method) (pyrosetta.rosetta.std.vector_core_scoring_hbonds_graph_HBondInfo method) (pyrosetta.rosetta.std.vector_core_scoring_sc__DOT method) (pyrosetta.rosetta.std.vector_core_scoring_sc_Atom method) (pyrosetta.rosetta.std.vector_double method) (pyrosetta.rosetta.std.vector_float method) (pyrosetta.rosetta.std.vector_int method) (pyrosetta.rosetta.std.vector_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.std.vector_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.vector_protocols_cluster_Cluster method) (pyrosetta.rosetta.std.vector_protocols_motif_grafting_movers_MotifMatch method) (pyrosetta.rosetta.std.vector_RDGeom_Point3D method) (pyrosetta.rosetta.std.vector_RDKit_Dict_Pair method) (pyrosetta.rosetta.std.vector_std_list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.std.vector_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_pair_std_shared_ptr_protocols_filters_Filter_protocols_filters_boolean_operations_t method) (pyrosetta.rosetta.std.vector_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_set_unsigned_long_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_fragment_FragSet_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_core_pose_Pose_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_cluster_calibur_Stru_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_protocols_hbnet_HBondNetStruct_t method) (pyrosetta.rosetta.std.vector_std_shared_ptr_std_list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.vector_std_string method) (pyrosetta.rosetta.std.vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_int_t method) (pyrosetta.rosetta.std.vector_std_vector_std_string_t method) (pyrosetta.rosetta.std.vector_std_vector_std_vector_double_t method) (pyrosetta.rosetta.std.vector_std_vector_unsigned_long_t method) (pyrosetta.rosetta.std.vector_unsigned_int method) (pyrosetta.rosetta.std.vector_unsigned_long method) (pyrosetta.rosetta.std.vector_utility_file_FileName method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Pair_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_map_std_string_t method) (pyrosetta.rosetta.std.vector_utility_json_spirit_Value_impl_utility_json_spirit_Config_vector_std_string_t method) (pyrosetta.rosetta.std.vector_utility_signals_Link method) (pyrosetta.rosetta.std.vector_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.std.vector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t method) (pyrosetta.rosetta.utility.vector0_core_conformation_ppo_torsion_bin method) (pyrosetta.rosetta.utility.vector0_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector0_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector0_double method) (pyrosetta.rosetta.utility.vector0_float method) (pyrosetta.rosetta.utility.vector0_int method) (pyrosetta.rosetta.utility.vector0_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector0_protocols_flexpack_interaction_graph_FlexbbSparseMatrixIndex method) (pyrosetta.rosetta.utility.vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector0_std_pair_float_float_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_antibody_grafting_SCS_Result_t method) (pyrosetta.rosetta.utility.vector0_std_shared_ptr_protocols_moves_Mover_t method) (pyrosetta.rosetta.utility.vector0_std_string method) (pyrosetta.rosetta.utility.vector0_unsigned_char method) (pyrosetta.rosetta.utility.vector0_unsigned_long method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_double_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_5_5_t method) (pyrosetta.rosetta.utility.vector0_utility_fixedsizearray1_double_16_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_core_io_AtomInformation_std_allocator_core_io_AtomInformation_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_list_std_shared_ptr_utility_SimulateMPIMessage_std_allocator_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.utility.vector0_utility_vector0_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector0_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Column method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_ForeignKey method) (pyrosetta.rosetta.utility.vector1_basic_database_schema_generator_Index method) (pyrosetta.rosetta.utility.vector1_basic_sampling_orientations_QuatDBMetadata method) (pyrosetta.rosetta.utility.vector1_bool method) (pyrosetta.rosetta.utility.vector1_char method) (pyrosetta.rosetta.utility.vector1_const_utility_vector1_int_std_allocator_int__star_t method) (pyrosetta.rosetta.utility.vector1_core_chemical_AA method) (pyrosetta.rosetta.utility.vector1_core_chemical_Adduct method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomICoor method) (pyrosetta.rosetta.utility.vector1_core_chemical_AtomType method) (pyrosetta.rosetta.utility.vector1_core_chemical_BondName method) (pyrosetta.rosetta.utility.vector1_core_chemical_io_merge_residue_behavior method) (pyrosetta.rosetta.utility.vector1_core_chemical_MutableResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResConnID method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueConnection method) (pyrosetta.rosetta.utility.vector1_core_chemical_ResidueProperty method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingConformer method) (pyrosetta.rosetta.utility.vector1_core_chemical_rings_RingSaturationType method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_GaussianParameter method) (pyrosetta.rosetta.utility.vector1_core_chemical_rna_PuckerState method) (pyrosetta.rosetta.utility.vector1_core_chemical_VariantType method) (pyrosetta.rosetta.utility.vector1_core_conformation_Atom method) (pyrosetta.rosetta.utility.vector1_core_conformation_PseudoBond method) (pyrosetta.rosetta.utility.vector1_core_conformation_signals_LengthEvent method) (pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_FragData method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_scores_VallFragmentScore method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallResidue method) (pyrosetta.rosetta.utility.vector1_core_fragment_picking_old_vall_VallSection method) (pyrosetta.rosetta.utility.vector1_core_fragment_rna_SYN_ANTI_RESTRICTION method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_bool_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_core_id_AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_core_id_DOF_ID method) (pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID method) (pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range method) (pyrosetta.rosetta.utility.vector1_core_io_AtomInformation method) (pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation method) (pyrosetta.rosetta.utility.vector1_core_io_LinkInformation method) (pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation method) (pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation method) (pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy method) (pyrosetta.rosetta.utility.vector1_core_io_SSBondInformation method) (pyrosetta.rosetta.utility.vector1_core_kinematics_AtomWithDOFChange method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Edge method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Jump method) (pyrosetta.rosetta.utility.vector1_core_kinematics_RT method) (pyrosetta.rosetta.utility.vector1_core_kinematics_Stub method) (pyrosetta.rosetta.utility.vector1_core_optimization_DerivCheckDataPoint method) (pyrosetta.rosetta.utility.vector1_core_optimization_DOF_DataPoint method) (pyrosetta.rosetta.utility.vector1_core_pack_annealer_PointDwell method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_double_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbond method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_buried_unsat_penalty_graph_BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) (pyrosetta.rosetta.utility.vector1_core_pack_guidance_scoreterms_sap_BlockParam method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_DotSphere method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_exposed_hydrophobic_data method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_RotamerDots method) (pyrosetta.rosetta.utility.vector1_core_pack_interaction_graph_SparseMatrixIndex method) (pyrosetta.rosetta.utility.vector1_core_pack_rotamer_set_ContinuousRotamerSet method) (pyrosetta.rosetta.utility.vector1_core_pack_scmin_ResidueAtomTreeCollectionMomento method) (pyrosetta.rosetta.utility.vector1_core_pack_task_operation_ResiduePDBIndexIs_ChainPos method) (pyrosetta.rosetta.utility.vector1_core_pack_task_ResidueLevelTask_ method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_AtomRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_PDBInfo_ResidueRecord method) (pyrosetta.rosetta.utility.vector1_core_pose_Pose method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_Atom_Bin method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BasePair method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_BaseStack method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Datum method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_Reactivity method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_RNA_SuiteInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo method) (pyrosetta.rosetta.utility.vector1_core_pose_UnrecognizedAtomRecord method) (pyrosetta.rosetta.utility.vector1_core_scoring_bin_transitions_BT_PROPERTIES method) (pyrosetta.rosetta.utility.vector1_core_scoring_CSA method) (pyrosetta.rosetta.utility.vector1_core_scoring_DC method) (pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair method) (pyrosetta.rosetta.utility.vector1_core_scoring_disulfides_DisulfideDerivativeAtom method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_Pairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_dssp_StrandPairing method) (pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector method) (pyrosetta.rosetta.utility.vector1_core_scoring_epr_deer_EPRSpinLabel method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_EtableParamsOnePair method) (pyrosetta.rosetta.utility.vector1_core_scoring_etable_etrie_GenericResidueConnectionData method) (pyrosetta.rosetta.utility.vector1_core_scoring_fiber_diffraction_OneGaussianScattering method) (pyrosetta.rosetta.utility.vector1_core_scoring_GenTorsionParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_Hairpin method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondEdge method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondNode method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBEvalTuple method) (pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_HBondWeightType method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_Loop method) (pyrosetta.rosetta.utility.vector1_core_scoring_loop_graph_LoopCycle method) (pyrosetta.rosetta.utility.vector1_core_scoring_mhc_epitope_energy_AlleleMatrix method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_MotifHit method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_ResPairMotif method) (pyrosetta.rosetta.utility.vector1_core_scoring_motif_Xfres method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pcs_PCSSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_pre_PRESingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_nmr_rdc_RDCSingle method) (pyrosetta.rosetta.utility.vector1_core_scoring_packing_Ball method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBall method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_CavityBallCluster method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_LR_MP_AtomData method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_SimplePDB_Atom method) (pyrosetta.rosetta.utility.vector1_core_scoring_packstat_Sphere method) (pyrosetta.rosetta.utility.vector1_core_scoring_power_diagram_SAnode method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC method) (pyrosetta.rosetta.utility.vector1_core_scoring_RDC_Rohl method) (pyrosetta.rosetta.utility.vector1_core_scoring_rna_RNA_Motif method) (pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmallAtNb method) (pyrosetta.rosetta.utility.vector1_core_scoring_SmoothScoreTermCoeffs method) (pyrosetta.rosetta.utility.vector1_core_scoring_SpringParams method) (pyrosetta.rosetta.utility.vector1_core_scoring_tableID method) (pyrosetta.rosetta.utility.vector1_core_select_residue_selector_ResidueRange method) (pyrosetta.rosetta.utility.vector1_core_sequence_Line method) (pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment method) (pyrosetta.rosetta.utility.vector1_double method) (pyrosetta.rosetta.utility.vector1_float method) (pyrosetta.rosetta.utility.vector1_int method) (pyrosetta.rosetta.utility.vector1_long method) (pyrosetta.rosetta.utility.vector1_numeric_CubicPolynomial method) (pyrosetta.rosetta.utility.vector1_numeric_geometry_hashing_Ball method) (pyrosetta.rosetta.utility.vector1_numeric_histograms_TwoDHistogram_unsigned_long_long_t method) (pyrosetta.rosetta.utility.vector1_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_BicubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_CubicSpline method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_interp_range method) (pyrosetta.rosetta.utility.vector1_numeric_interpolation_spline_Point method) (pyrosetta.rosetta.utility.vector1_numeric_MultiDimensionalHistogram method) (pyrosetta.rosetta.utility.vector1_numeric_random_WeightedSampler method) (pyrosetta.rosetta.utility.vector1_numeric_RocPoint method) (pyrosetta.rosetta.utility.vector1_numeric_urs_Quat method) (pyrosetta.rosetta.utility.vector1_numeric_xyzMatrix_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzTransform_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray1D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_double_t method) (pyrosetta.rosetta.utility.vector1_ObjexxFCL_FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_AlternativePairings method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_ClassicAbinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_PairingStatEntry method) (pyrosetta.rosetta.utility.vector1_protocols_abinitio_StageID method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_AntibodyNumberingSchemeEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRDefinitionEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_CDRNameEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_CDRClusterEnum method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_clusters_ClusterData method) (pyrosetta.rosetta.utility.vector1_protocols_antibody_design_PDBNumbering method) (pyrosetta.rosetta.utility.vector1_protocols_backbone_moves_local_backbone_mover_Residue method) (pyrosetta.rosetta.utility.vector1_protocols_backrub_BackrubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef1 method) (pyrosetta.rosetta.utility.vector1_protocols_branch_angle_BranchCoef2 method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_DbTrajectoryRecorder_Frame method) (pyrosetta.rosetta.utility.vector1_protocols_canonical_sampling_TorsionSpec method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_CartesianAtom method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Angle method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_Bond method) (pyrosetta.rosetta.utility.vector1_protocols_cartesian_MD_HarmonicDihedral method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_DataPoint method) (pyrosetta.rosetta.utility.vector1_protocols_cluster_Exemplar method) (pyrosetta.rosetta.utility.vector1_protocols_constraints_additional_ConstraintEvaluator method) (pyrosetta.rosetta.utility.vector1_protocols_contact_map_Contact method) (pyrosetta.rosetta.utility.vector1_protocols_cyclic_peptide_PSM_StubMode method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_BondInfo method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution method) (pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_StructureSlice method) (pyrosetta.rosetta.utility.vector1_protocols_features_TaskOperationFeatures_Taskop_id_name_factory_ method) (pyrosetta.rosetta.utility.vector1_protocols_fold_from_loops_utils_NubSegment method) (pyrosetta.rosetta.utility.vector1_protocols_forge_build_Interval method) (pyrosetta.rosetta.utility.vector1_protocols_frag_picker_LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.utility.vector1_protocols_helical_bundle_BPC_Parameters method) (pyrosetta.rosetta.utility.vector1_protocols_hotspot_hashing_VectorPair method) (pyrosetta.rosetta.utility.vector1_protocols_hybridization_detailedControlsTagSetting method) (pyrosetta.rosetta.utility.vector1_protocols_indexed_structure_store_BackboneStub method) (pyrosetta.rosetta.utility.vector1_protocols_jd2_archive_Batch method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_chunk_library_ChunkLibraryPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_dag_node_managers_ResultElements method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_full_model_FullModelPreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jd3_standard_PreliminaryLarvalJob method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_DisulfPairing method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSelector_JumpWeightDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_JumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_jumping_ResiduePairJumpSetup_JumpDef method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewAtom method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewResidue method) (pyrosetta.rosetta.utility.vector1_protocols_legacy_sewing_SewSegment method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_ReweightableRepEnergy method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionDistrParams method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ligand_options_InterfaceInfo method) (pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolution method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_LoopPartialSolutionStore method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_ResTorsions method) (pyrosetta.rosetta.utility.vector1_protocols_loop_grower_SheetPositions method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loop method) (pyrosetta.rosetta.utility.vector1_protocols_loops_LoopFromFileData method) (pyrosetta.rosetta.utility.vector1_protocols_loops_Loops method) (pyrosetta.rosetta.utility.vector1_protocols_loops_SerializedLoop method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_CentroidRotNum method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_RotData method) (pyrosetta.rosetta.utility.vector1_protocols_make_rot_lib_TorsionRange method) (pyrosetta.rosetta.utility.vector1_protocols_match_Hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_match_dspos1 method) (pyrosetta.rosetta.utility.vector1_protocols_match_ProbeRadius method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_BuildSet method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_hit method) (pyrosetta.rosetta.utility.vector1_protocols_match_upstream_SampleStrategyData method) (pyrosetta.rosetta.utility.vector1_protocols_md_Constraint method) (pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix method) (pyrosetta.rosetta.utility.vector1_protocols_membrane_SpanInfo method) (pyrosetta.rosetta.utility.vector1_protocols_monte_carlo_AcceptedScores method) (pyrosetta.rosetta.utility.vector1_protocols_motif_grafting_movers_motif2scaffold_indexes method) (pyrosetta.rosetta.utility.vector1_protocols_moves_TrialCounter method) (pyrosetta.rosetta.utility.vector1_protocols_mpi_refinement_MethodParams method) (pyrosetta.rosetta.utility.vector1_protocols_multistate_design_SingleStateEntityData method) (pyrosetta.rosetta.utility.vector1_protocols_nonlocal_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_optimize_weights_WeightRangeConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_pack_daemon_StructureFileNames method) (pyrosetta.rosetta.utility.vector1_protocols_pdbinfo_manipulations_SequenceSpecification method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_Mutant method) (pyrosetta.rosetta.utility.vector1_protocols_pmut_scan_MutationData method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_MergePDBMover_Overlap method) (pyrosetta.rosetta.utility.vector1_protocols_pose_creation_SliceToMiniProteinMover_Chunk method) (pyrosetta.rosetta.utility.vector1_protocols_pose_metric_calculators_EnergiesData method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_mutt method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_SecretionOptimizationMover_tm_region method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_movers_VLBInstruction method) (pyrosetta.rosetta.utility.vector1_protocols_protein_interface_design_Transformation method) (pyrosetta.rosetta.utility.vector1_protocols_qsar_ColorGradient method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBResidueRange method) (pyrosetta.rosetta.utility.vector1_protocols_rbsegment_relax_RBSegment method) (pyrosetta.rosetta.utility.vector1_protocols_recces_Histogram method) (pyrosetta.rosetta.utility.vector1_protocols_relax_DatabaseRelaxScript method) (pyrosetta.rosetta.utility.vector1_protocols_rigid_Partner method) (pyrosetta.rosetta.utility.vector1_protocols_rosetta_scripts_ParsedProtocol_ParsedProtocolStep method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsEnergyParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsGridSearchParameter method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_data_per_lanthanides method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs_PCS_line_data method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_data_per_lanthanides_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs1_PCS_line_data_Ts1 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_data_per_lanthanides_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs3_PCS_line_data_Ts3 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_data_per_lanthanides_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs4_PCS_line_data_Ts4 method) (pyrosetta.rosetta.utility.vector1_protocols_seeded_abinitio_SegmentSpec method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_ContactDescription method) (pyrosetta.rosetta.utility.vector1_protocols_sewing_data_storage_LigandDescription method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_Quat method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_RegionalConnections method) (pyrosetta.rosetta.utility.vector1_protocols_simple_filters_ResidueDepthFrag method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_IonizableResidue method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_LoggedFragmentMover_Item method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_TorsionPerturbType method) (pyrosetta.rosetta.utility.vector1_protocols_simple_moves_WaterRot method) (pyrosetta.rosetta.utility.vector1_protocols_splice_BBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_splice_ResidueBBDofs method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_Combine_Tags_Info method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_modeler_rna_phosphate_PhosphateMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_Attachment method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_monte_carlo_mover_StepWiseMove method) (pyrosetta.rosetta.utility.vector1_protocols_stepwise_sampler_copy_dofs_ResidueAlternativeSet method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_CstResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_ResInteractions method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_match_enzdes_util_SingleConstraint method) (pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint method) (pyrosetta.rosetta.utility.vector1_protocols_trajectory_DbTrajectoryWriter_Frame method) (pyrosetta.rosetta.utility.vector1_short method) (pyrosetta.rosetta.utility.vector1_signed_char method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_downstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std__Rb_tree_const_iterator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_std_array_int_3_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_std_shared_ptr_const_protocols_match_downstream_SecMatchResiduePairEvaluator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_const_numeric_expression_parser_Expression_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_shared_ptr_protocols_pack_daemon_NPDPropCalculator_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_pair_unsigned_long_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.utility.vector1_std_list_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_list_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_char_double_std_less_char_std_allocator_std_pair_const_char_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_core_chemical_AA_utility_vector1_double_std_allocator_double_std_less_core_chemical_AA_std_allocator_std_pair_const_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_cstType_unsigned_long_std_less_protocols_jumping_cstType_std_allocator_std_pair_const_protocols_jumping_cstType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_protocols_jumping_dofType_unsigned_long_std_less_protocols_jumping_dofType_std_allocator_std_pair_const_protocols_jumping_dofType_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_shared_ptr_const_core_conformation_Residue_double_std_less_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_pair_const_std_shared_ptr_const_core_conformation_Residue_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_bool_std_less_std_string_std_allocator_std_pair_const_std_string_bool_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_id_NamedAtomID_std_less_std_string_std_allocator_std_pair_const_std_string_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_core_io_pdb_Field_std_less_std_string_std_allocator_std_pair_const_std_string_core_io_pdb_Field_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_map_std_string_unsigned_long_std_less_std_string_std_allocator_std_pair_const_std_string_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_core_chemical_AA_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_core_chemical_AA_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_std_shared_ptr_protocols_frag_picker_CandidatesCollector_t method) (pyrosetta.rosetta.utility.vector1_std_map_unsigned_long_unsigned_long_std_less_unsigned_long_std_allocator_std_pair_const_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_std_less_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_std_pair_const_utility_keys_Key2Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_map_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_std_less_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_std_pair_const_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_std_pair_bool_bool_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_core_kinematics_Jump_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_std_pair_core_id_AtomID_core_id_AtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_DOF_ID_double_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_NamedAtomID_core_id_NamedAtomID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_core_id_TorsionID_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_id_TorsionID_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t method) (pyrosetta.rosetta.utility.vector1_std_pair_core_io_raw_data_DisulfideFile_ResNum_core_io_raw_data_DisulfideFile_ResNum_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_std_allocator_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_std_allocator_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_jd3_JGJobNode_std_allocator_std_shared_ptr_protocols_jd3_JGJobNode_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_std_allocator_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_std_allocator_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_std_allocator_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_std_allocator_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_std_allocator_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_std_allocator_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) pop_back() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HPool_RMSD method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.Pool_RMSD method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) pop_back_CA_xyz() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) pop_front() (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) pop_job_from_queue() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) pop_mutation() (pyrosetta.rosetta.protocols.pmut_scan.Mutant method) pop_next() (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) pop_next_message_for_node_of_type() (pyrosetta.rosetta.utility.SimulateMPIData method) pop_next_message_of_type() (pyrosetta.rosetta.utility.SimulateMPIData method) pop_node() (pyrosetta.rosetta.utility.tag.XMLErrorHandler method) pop_passport() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) popcount_until_bit() (in module pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome) popitem() (pyrosetta.bindings.pose.PoseScoreAccessor method) (pyrosetta.io.silent_file_map.SilentFileMap method) populate() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.DsspShiftArray method) populate_all_cdrs() (pyrosetta.rosetta.protocols.antibody_legacy.Antibody method) populate_all_OP_vector() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) populate_from_pdb_list() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) populate_from_segment_file() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) populate_from_segment_file_and_get_random_vector_set() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) populate_results_from_db() (in module pyrosetta.rosetta.protocols.antibody.grafting) population (pyrosetta.rosetta.core.chemical.carbohydrates.LinkageConformerData property) population() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) population_size() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) pore_center_x() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) pore_center_x_deriv() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) pore_center_y() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) pore_center_y_deriv() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) pore_major_radius() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) pore_major_radius_deriv() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) pore_minor_radius() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) pore_minor_radius_deriv() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) pore_radius() (pyrosetta.rosetta.core.select.util.SelectResiduesByLayer method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) pore_rotation() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) (pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo method) pore_rotation_deriv() (pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters method) pos() (pyrosetta.rosetta.protocols.forge.build.GrowLeft method) (pyrosetta.rosetta.protocols.forge.build.GrowRight method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) pos1 (pyrosetta.rosetta.protocols.jumping.DisulfPairing property) Pos1() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) pos1() (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) pos2 (pyrosetta.rosetta.protocols.jumping.DisulfPairing property) Pos2() (pyrosetta.rosetta.core.scoring.dssp.Pairing method) pos2() (pyrosetta.rosetta.protocols.environment.claims.JumpClaim method) pos_ (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs.ChainPos property) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt.ChainPos property) pos_in_history_queue() (pyrosetta.rosetta.utility.recent_history_queue method) pos_mod() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.protocols.cryst) Pose (class in pyrosetta.rosetta.core.pose) pose (pyrosetta.bindings.pose.PoseResidueLabelAccessor attribute) (pyrosetta.bindings.pose.PoseScoreAccessor attribute) (pyrosetta.distributed.packed_pose.core.PackedPose property) (pyrosetta.rosetta.protocols.antibody.CDRDBPose property) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder.Frame property) (pyrosetta.rosetta.protocols.environment.EnvClaimBroker.BrokerResult property) POSE (pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum attribute) pose (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.PoseForPoseID property) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover.Chunk property) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryWriter.Frame property) pose() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.import_pose.PoseResource method) (pyrosetta.rosetta.core.import_pose.RNA_DeNovoSetup method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pose.datacache.CacheablePoseRawPtr method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobResult method) (pyrosetta.rosetta.protocols.jd3.chunk_library.MoverAndChunkLibraryJob method) (pyrosetta.rosetta.protocols.jd3.job_results.PoseJobResult method) (pyrosetta.rosetta.protocols.jd3.jobs.MoverJob method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) (pyrosetta.rosetta.protocols.multistate_design.PackingState method) (pyrosetta.rosetta.protocols.multistate_design.SingleState method) (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) (pyrosetta.rosetta.protocols.sic_dock.Rose method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeSet method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) pose0() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) pose1() (pyrosetta.rosetta.core.scoring.motif.MotifHit method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) pose1_ (pyrosetta.rosetta.core.scoring.motif.MotifHit property) pose1_has_most_CBs() (in module pyrosetta.rosetta.protocols.sic_dock) pose1ptr() (pyrosetta.rosetta.core.scoring.motif.MotifHit method) pose2() (pyrosetta.rosetta.core.scoring.motif.MotifHit method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifQuery method) pose2_ (pyrosetta.rosetta.core.scoring.motif.MotifHit property) pose2pdb() (pyrosetta.rosetta.core.pose.PDBInfo method) pose2ptr() (pyrosetta.rosetta.core.scoring.motif.MotifHit method) pose_ (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator property) (pyrosetta.rosetta.protocols.electron_density.RefinementResult property) pose_aligner() (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) pose_at_origin() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) pose_atom (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator.MappedAtom property) POSE_BEFORE_CAVITIES_ADDED (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) pose_cache_real_data (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) pose_cache_real_data() (pyrosetta.rosetta.core.io.StructFileRep method) pose_cache_string_data (pyrosetta.rosetta.core.io.mmtf.ExtraDataEnum attribute) pose_cache_string_data() (pyrosetta.rosetta.core.io.StructFileRep method) pose_charge() (in module pyrosetta.rosetta.protocols.antibody) pose_coords_are_same() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) pose_coords_as_cols() (in module pyrosetta.toolbox.extract_coords_pose) pose_coords_as_rows() (in module pyrosetta.toolbox.extract_coords_pose) pose_cop() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) POSE_COPY (pyrosetta.rosetta.basic.ProfTag attribute) pose_data_cache_from_sfr() (in module pyrosetta.rosetta.core.io) pose_deep_copy() (pyrosetta.rosetta.core.import_pose.PoseResource method) pose_energies_from_sfr() (in module pyrosetta.rosetta.core.io) pose_energies_to_json() (in module pyrosetta.rosetta.protocols.rpc) pose_energy() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_JobResultsSummary method) pose_from_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) pose_from_checkpoint_file() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) pose_from_checkpoint_file_low() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) pose_from_file() (in module pyrosetta.distributed.io) (in module pyrosetta.rosetta.core.import_pose) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter method) pose_from_input_source() (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputter method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter method) pose_from_job() (pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobInputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobInputter method) (pyrosetta.rosetta.protocols.jd2.BatchJobInputter method) (pyrosetta.rosetta.protocols.jd2.EmptyPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.EnsembleJobInputter method) (pyrosetta.rosetta.protocols.jd2.JobInputter method) (pyrosetta.rosetta.protocols.jd2.LargeNstructJobInputter method) (pyrosetta.rosetta.protocols.jd2.LazySilentFileJobInputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobInputter method) (pyrosetta.rosetta.protocols.jd2.PoseInputStreamJobInputter method) (pyrosetta.rosetta.protocols.jd2.ScreeningJobInputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobInputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobInputter method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibJobInputter method) (pyrosetta.rosetta.protocols.protein_interface_design.ParserJobInputter method) pose_from_pdb() (in module pyrosetta.io) pose_from_pdb_stream() (in module pyrosetta.rosetta.core.import_pose) pose_from_pdbstring() (in module pyrosetta.distributed.io) (in module pyrosetta.rosetta.core.import_pose) pose_from_pose() (in module pyrosetta.rosetta.core.io) pose_from_rcsb() (in module pyrosetta.toolbox.rcsb) pose_from_res() (pyrosetta.rosetta.protocols.splice.SpliceManager method) pose_from_saccharide_sequence() (in module pyrosetta.rosetta.core.pose) pose_from_sequence() (in module pyrosetta.distributed.io) (in module pyrosetta.io) pose_from_store() (in module pyrosetta.rosetta.protocols.indexed_structure_store) pose_has_nonzero_Bs() (in module pyrosetta.rosetta.core.scoring.electron_density) pose_id (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.PoseForPoseID property) pose_id() (pyrosetta.rosetta.protocols.jd3.deallocation.InputPoseDeallocationMessage method) pose_idx_ (pyrosetta.rosetta.protocols.electron_density.RBfitResult property) pose_index() (pyrosetta.rosetta.core.pose.ResidueIndexDescriptionPoseNum method) pose_input_stream() (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) pose_inputter (pyrosetta.rosetta.protocols.jd3.standard.PreliminaryLarvalJob property) pose_inputter_creators() (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory method) pose_inputter_xml_schema_group_name() (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory static method) pose_inputter_xsd_type_definition_w_attributes() (in module pyrosetta.rosetta.protocols.jd3.pose_inputters) pose_length() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) pose_list (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) pose_list() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeSet method) pose_loop_anchors() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) pose_matches_user_tag() (in module pyrosetta.rosetta.protocols.jobdist) pose_max_nbr_radius() (in module pyrosetta.rosetta.core.pose) pose_minobj() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) pose_name (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) pose_name() (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) pose_num() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) pose_numb() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) pose_number() (pyrosetta.rosetta.protocols.legacy_sewing.Model method) pose_outputter_creators() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) pose_outputter_from_command_line() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) pose_outputter_xml_schema_group_name() (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory static method) pose_outputter_xsd_type_definition_w_attributes() (in module pyrosetta.rosetta.protocols.jd3.pose_outputters) pose_passes_ss_length_check() (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) pose_preliminaries() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) pose_raw_unfolded_state_energymap() (pyrosetta.rosetta.core.scoring.UnfoldedStatePotential method) pose_ref() (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) pose_reporter_group_name() (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory static method) pose_res_no() (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) pose_residue() (pyrosetta.rosetta.protocols.denovo_design.components.StructureData method) pose_residue_is_terminal() (in module pyrosetta.rosetta.core.pose) pose_resnum() (pyrosetta.rosetta.protocols.pmut_scan.MutationData method) pose_right() (pyrosetta.rosetta.protocols.forge.build.ConnectRight method) (pyrosetta.rosetta.protocols.forge.build.RelativeConnectRight method) pose_segment_ends (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFGMSettings property) pose_segment_starts (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFGMSettings property) POSE_SELECTION (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) pose_selection_by_full_score() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) pose_selector_group_name() (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory static method) POSE_SEQUENCE (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) pose_sequence() (pyrosetta.rosetta.core.energy_methods.PoseSequence method) pose_setup_from_file() (in module pyrosetta.rosetta.protocols.recces) pose_setup_turner() (in module pyrosetta.rosetta.protocols.recces) pose_spherical_samples() (in module pyrosetta.rosetta.protocols.electron_density) pose_tag() (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputSpecification method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputSpecification method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) pose_tilt_angle_and_center_distance() (in module pyrosetta.rosetta.protocols.membrane) pose_tm_com() (in module pyrosetta.rosetta.protocols.membrane) pose_to_pack_data() (in module pyrosetta.rosetta.core.scoring.packstat) pose_to_pdb() (in module pyrosetta.rosetta.core.pose) pose_to_res() (pyrosetta.rosetta.protocols.splice.SpliceManager method) pose_to_segment() (pyrosetta.rosetta.protocols.denovo_design.components.Segment method) pose_with_most_CBs() (in module pyrosetta.rosetta.protocols.sic_dock) PoseArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) PoseArchitectCreator (class in pyrosetta.rosetta.protocols.denovo_design.architects) PoseBalls (class in pyrosetta.rosetta.core.scoring.packing) PoseBallsLite (class in pyrosetta.rosetta.core.scoring.packing) poseBfacts2multivec() (pyrosetta.rosetta.protocols.electron_density.BfactorMultifunc method) PoseBuilder (class in pyrosetta.rosetta.protocols.denovo_design.components) PoseComment (class in pyrosetta.rosetta.protocols.simple_filters) PoseCommentFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) PoseCommentsFeatures (class in pyrosetta.rosetta.protocols.features) PoseCommentsFeaturesCreator (class in pyrosetta.rosetta.protocols.features) PoseCondition (class in pyrosetta.rosetta.protocols.moves) PoseConformationFeatures (class in pyrosetta.rosetta.protocols.features) PoseConformationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) poseCoord (class in pyrosetta.rosetta.core.scoring.electron_density) PoseCoordPickMode (class in pyrosetta.rosetta.core.pose) PoseCoordPickMode_ALL (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_BB (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_BNP (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_CA (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_CB (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_CB_else_CA (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_CBorCA (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_HVY (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_HVY_IF_NP (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_N_C_O (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_N_CA_C (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_N_CA_C_CB (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_NBR (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseCoordPickMode_NUL (pyrosetta.rosetta.core.pose.PoseCoordPickMode attribute) PoseEvaluator (class in pyrosetta.rosetta.protocols.evaluation) PoseFolder (class in pyrosetta.rosetta.protocols.denovo_design.components) PoseForPoseID (class in pyrosetta.rosetta.protocols.multistage_rosetta_scripts) PoseFoundResiduesCombination (class in pyrosetta.rosetta.protocols.enzdes) PoseFromPoseResourceMover (class in pyrosetta.rosetta.protocols.simple_moves) PoseFromPoseResourceMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) PoseFromSequenceMover (class in pyrosetta.rosetta.protocols.pose_creation) PoseFromSequenceMoverCreator (class in pyrosetta.rosetta.protocols.pose_creation) PoseFromSFRBuilder (class in pyrosetta.rosetta.core.io.pose_from_sfr) PoseInfoFilter (class in pyrosetta.rosetta.protocols.simple_filters) PoseInfoFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) PoseInputSource (class in pyrosetta.rosetta.protocols.jd3.pose_inputters) PoseInputStream (class in pyrosetta.rosetta.core.import_pose.pose_stream) PoseInputStreamJobInputter (class in pyrosetta.rosetta.protocols.jd2) PoseInputStreamJobInputterCreator (class in pyrosetta.rosetta.protocols.jd2) PoseInputter (class in pyrosetta.rosetta.protocols.jd3.pose_inputters) PoseInputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_inputters) PoseInputterFactory (class in pyrosetta.rosetta.protocols.jd3.pose_inputters) PoseInserter (class in pyrosetta.rosetta.protocols.match.output) PoseJobResult (class in pyrosetta.rosetta.protocols.jd3.job_results) PoseMatchOutputWriter (class in pyrosetta.rosetta.protocols.match.output) PoseMetricCalculator (class in pyrosetta.rosetta.core.pose.metrics) PoseMetricContainer (class in pyrosetta.rosetta.core.pose.metrics) PoseNumberedLoopFileReader (class in pyrosetta.rosetta.protocols.loops) poseOP (pyrosetta.rosetta.protocols.pose_length_moves.Chain property) poseOPs_from_files() (in module pyrosetta.rosetta.core.import_pose) PoseOutputSpecification (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) PoseOutputter (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) PoseOutputterCreator (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) PoseOutputterFactory (class in pyrosetta.rosetta.protocols.jd3.pose_outputters) PosePackData (class in pyrosetta.rosetta.core.scoring.packstat) PosePropertyReporter (class in pyrosetta.rosetta.protocols.rosetta_scripts) PosePropertyReporterCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) PosePropertyReporterFactory (class in pyrosetta.rosetta.protocols.rosetta_scripts) PoseResidueAccessor (class in pyrosetta.bindings.pose) PoseResidueLabelAccessor (class in pyrosetta.bindings.pose) PoseResidueLabelMaskAccessor (class in pyrosetta.bindings.pose) PoseResidueTypeSet (class in pyrosetta.rosetta.core.chemical) PoseResource (class in pyrosetta.rosetta.core.import_pose) PoseResourceLoader (class in pyrosetta.rosetta.core.import_pose) PoseResourceLoaderCreator (class in pyrosetta.rosetta.core.import_pose) poses (pyrosetta.io.silent_file_map.SilentFileMap property) poses_from_cmd_line() (in module pyrosetta.rosetta.protocols.comparative_modeling) poses_from_files() (in module pyrosetta.io) (in module pyrosetta.rosetta.core.import_pose) poses_from_sequences() (in module pyrosetta.io) poses_from_silent() (in module pyrosetta.distributed.io) (in module pyrosetta.io) poses_to_silent() (in module pyrosetta.io) PoseScoreAccessor (class in pyrosetta.bindings.pose) PoseSegment (class in pyrosetta.rosetta.protocols.pose_sewing.data_storage) PoseSelectionScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) PoseSelector (class in pyrosetta.rosetta.protocols.rosetta_scripts) PoseSelectorCreator (class in pyrosetta.rosetta.protocols.rosetta_scripts) PoseSelectorFactory (class in pyrosetta.rosetta.protocols.rosetta_scripts) PoseSelectorFlags (class in pyrosetta.rosetta.protocols.rosetta_scripts) PoseSequence (class in pyrosetta.rosetta.core.energy_methods) PoseSphericalSamplesOptions (class in pyrosetta.rosetta.protocols.electron_density) PoseToStructFileRepConverter (class in pyrosetta.rosetta.core.io.pose_to_sfr) PoseWithTerminalSegmentsOfKnownDSSP (class in pyrosetta.rosetta.protocols.pose_sewing.data_storage) position (pyrosetta.rosetta.core.conformation.signals.IdentityEvent property) (pyrosetta.rosetta.core.conformation.signals.LengthEvent property) (pyrosetta.rosetta.core.scoring.lkball.ScoredBridgingWater property) (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) (pyrosetta.rosetta.protocols.dna.PositionType property) (pyrosetta.rosetta.protocols.hotspot_hashing.VectorPair property) position() (pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom method) (pyrosetta.rosetta.core.environment.LocalPosition method) (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) (pyrosetta.rosetta.core.pose.rna.RNA_Datum method) (pyrosetta.rosetta.core.pose.rna.RNA_Reactivity method) (pyrosetta.rosetta.core.scoring.motif.Xfrag method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) position_ala_ddG() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) POSITION_CONSERVED_RESIDUES (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) position_cutpoint_phosphate_torsions() (in module pyrosetta.rosetta.core.pose.rna) position_five_prime_phosphate() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate) position_index() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) position_of_atom_on_ring() (in module pyrosetta.rosetta.core.conformation) position_stub() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) position_untouchable() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) position_vector_setup() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) PositionConservedResiduesStore (class in pyrosetta.rosetta.core.pose.datacache) PositionDdGInfo (class in pyrosetta.rosetta.core.io.PositionDdGInfo) positions() (pyrosetta.rosetta.protocols.dna.DnaChains method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) positions_in_secstruct() (in module pyrosetta.rosetta.protocols.simple_filters) positions_incompatible_with_task() (in module pyrosetta.rosetta.protocols.backrub) PositionSpecificRandomizer (class in pyrosetta.rosetta.protocols.genetic_algorithm) PositionType (class in pyrosetta.rosetta.protocols.dna) positive() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) POSITIVE_CHARGE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) positive_pow() (in module pyrosetta.rosetta.core.pack.dunbrack) positive_value() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) possible_mutants (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover.tm_region property) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter.tm_region property) possible_root() (in module pyrosetta.rosetta.protocols.rna.denovo) (pyrosetta.rosetta.core.kinematics.FoldTree method) possible_working_res_1 (pyrosetta.rosetta.protocols.stepwise.modeler.rna.InternalWorkingResidueParameter property) possible_working_res_2 (pyrosetta.rosetta.protocols.stepwise.modeler.rna.InternalWorkingResidueParameter property) PossibleAtomTypesForAtom (class in pyrosetta.rosetta.core.chemical.gasteiger) PossibleLoop (class in pyrosetta.rosetta.protocols.pose_length_moves) possibly_canonical() (in module pyrosetta.rosetta.core.chemical.rna)

possibly_canonical_strict() (in module pyrosetta.rosetta.core.chemical.rna) post_catalog_op() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) post_decoy() (in module pyrosetta.rosetta.protocols.network) post_decrement() (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) post_file() (in module pyrosetta.rosetta.protocols.network) post_increment() (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) post_loop_closure_protocol() (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) POST_METHYLENE_META_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) POST_METHYLENE_ORTHO_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) POST_METHYLENE_PARA_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) post_process() (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) post_relax_round_update_steps() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) post_trans_ (pyrosetta.rosetta.protocols.electron_density.RBfitResult property) PostDockAssemblyScorer (class in pyrosetta.rosetta.protocols.domain_assembly) postgres (pyrosetta.rosetta.utility.sql_database.DatabaseMode attribute) (pyrosetta.rosetta.utility.sql_database.DatabaseMode.e attribute) PosType (class in pyrosetta.rosetta.protocols.multistate_design) PosTypeCreator (class in pyrosetta.rosetta.protocols.multistate_design) potential_energy() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) potential_twobody_memory_use() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) potential_valid_ss_strings() (pyrosetta.rosetta.protocols.indexed_structure_store.SSHashedFragmentStore method) pow() (in module pyrosetta.rosetta.ObjexxFCL) power() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) power_distance() (in module pyrosetta.rosetta.core.scoring.power_diagram) PowerDiagram (class in pyrosetta.rosetta.core.scoring.power_diagram) PowExpression (class in pyrosetta.rosetta.protocols.pack_daemon) PP() (in module pyrosetta.rosetta.numeric.crick_equations) ppk_only (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) ppo_torbin_A (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torbin_a (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torbin_B (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torbin_b (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torbin_E (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torbin_e (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torbin_G (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torbin_g (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torbin_U (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torbin_X (pyrosetta.rosetta.core.conformation.ppo_torsion_bin attribute) ppo_torsion_bin (class in pyrosetta.rosetta.core.conformation) pptr() (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) PQR (class in pyrosetta.rosetta.core.scoring) Pr (pyrosetta.rosetta.core.chemical.element.Elements attribute) pr_idx_ (pyrosetta.rosetta.core.scoring.packstat.MultiProbePerSphereAccumulator property) (pyrosetta.rosetta.core.scoring.packstat.MultiProbePoseAccumulator property) PR_UDPServer (class in pyrosetta.network.rosetta_udp_to_tcp_bridge) pre_align() (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) pre_catalog_op() (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.ABEGOEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.EnergyEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.IdentityEval method) (pyrosetta.rosetta.core.fragment.picking_old.vall.eval.VallFragmentEval method) pre_chitip_transform() (pyrosetta.rosetta.protocols.match.upstream.UpstreamResTypeGeometry method) pre_cyc_pose (pyrosetta.rosetta.protocols.peptide_deriver.CyclizedPeptideInfo property) pre_decrement() (pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileData.iterator method) (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) (pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter method) (pyrosetta.rosetta.utility.graph.LowMemEdgeListIter method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_MResIDSize_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_NodeIDSize_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_RotamerIDSize_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_NStructIndex_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_PrelimJobNodeID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_ResultIndex_t method) pre_erf_opt_tau() (in module pyrosetta.rosetta.core.scoring.nmr.pre) pre_erf_opt_tau_xyz() (in module pyrosetta.rosetta.core.scoring.nmr.pre) pre_increment() (pyrosetta.rosetta.core.fragment.ConstFrameIterator method) (pyrosetta.rosetta.core.fragment.FragID_Iterator method) (pyrosetta.rosetta.core.fragment.FrameIterator method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.DecoyFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.RawFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.RawFileData.iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.const_iterator method) (pyrosetta.rosetta.core.io.raw_data.ScoreFileData.iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileData.const_iterator method) (pyrosetta.rosetta.core.io.silent.SilentFileData.iterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.constraints.CstResNeighbIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.DenseNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.CentroidDisulfideNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingNeighborIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbConstIterator method) (pyrosetta.rosetta.core.scoring.disulfides.DisulfResNeighbIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.OneToAllNeighborIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.PolymerBondedNeighborIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborConstIterator method) (pyrosetta.rosetta.core.scoring.ResidueNeighborIterator method) (pyrosetta.rosetta.core.select.Enumerate1WithSelector method) (pyrosetta.rosetta.ObjexxFCL.byte method) (pyrosetta.rosetta.ObjexxFCL.ubyte method) (pyrosetta.rosetta.protocols.match.VoxelSetIterator method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.utility.Enumerate1 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) (pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter method) (pyrosetta.rosetta.utility.graph.LowMemEdgeListIter method) (pyrosetta.rosetta.utility.LexicographicalIterator method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_MResIDSize_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_NodeIDSize_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_RotamerIDSize_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_GlobalJobID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_JobDAGNodeID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_NStructIndex_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_PrelimJobNodeID_t method) (pyrosetta.rosetta.utility.StrongT_unsigned_long_protocols_jd3_ResultIndex_t method) pre_load_data() (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) pre_loop_closure_protocol() (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) PRE_METHYLENE_META_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PRE_METHYLENE_ORTHO_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PRE_METHYLENE_PARA_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PRE_METHYLENE_POST_METHYLENE_META_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) pre_packminpack() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) pre_process() (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.topology_broker.AsymFoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.BasicJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CoordConstraintClaimer method) (pyrosetta.rosetta.protocols.topology_broker.CutBiasClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DensityScoringClaimer method) (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FibrilModelingClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FoldandDockClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.LoopFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MembraneTopologyClaimer method) (pyrosetta.rosetta.protocols.topology_broker.MetalloClaimer method) (pyrosetta.rosetta.protocols.topology_broker.PcsEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts1 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts2 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts3 method) (pyrosetta.rosetta.protocols.topology_broker.PseudocontactShiftEnergyController_Ts4 method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SequenceClaimer method) (pyrosetta.rosetta.protocols.topology_broker.StartStructClaimer method) (pyrosetta.rosetta.protocols.topology_broker.SymmetryClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TMHTopologySamplerClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TopologyClaimer method) PRE_RATE_TYPE (class in pyrosetta.rosetta.core.scoring.nmr) pre_rate_type_to_string() (pyrosetta.rosetta.core.scoring.nmr.pre.PRESingleSet method) pre_relax_round_update_steps() (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) pre_scoring() (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) PRE_SPIN_TYPE (class in pyrosetta.rosetta.core.scoring.nmr) PRE_SPIN_TYPE_C (pyrosetta.rosetta.core.scoring.nmr.PRE_SPIN_TYPE attribute) pre_spin_type_from_atom_name() (in module pyrosetta.rosetta.core.scoring.nmr) PRE_SPIN_TYPE_H (pyrosetta.rosetta.core.scoring.nmr.PRE_SPIN_TYPE attribute) PRE_SPIN_TYPE_N (pyrosetta.rosetta.core.scoring.nmr.PRE_SPIN_TYPE attribute) pre_tracer_process() (in module pyrosetta.rosetta.basic.options) pre_trans_ (pyrosetta.rosetta.protocols.electron_density.RBfitResult property) prealigned_input() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner method) preallocate() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) preamble() (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBase method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction method) preapply() (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) precalculate_bb_bb_energy_for_design() (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.scoring.geometric_solvation.GeometricSolEnergyEvaluator method) precision() (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.numeric.IOTraits_double_t static method) (pyrosetta.rosetta.numeric.IOTraits_float_t static method) (pyrosetta.rosetta.numeric.IOTraits_int_t static method) (pyrosetta.rosetta.numeric.IOTraits_long_double_t static method) (pyrosetta.rosetta.numeric.IOTraits_long_t static method) (pyrosetta.rosetta.numeric.IOTraits_short_t static method) (pyrosetta.rosetta.numeric.IOTraits_unsigned_int_t static method) (pyrosetta.rosetta.numeric.IOTraits_unsigned_long_t static method) (pyrosetta.rosetta.numeric.IOTraits_unsigned_short_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_double_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_float_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_int_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_long_double_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_long_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_short_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_int_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_long_t static method) (pyrosetta.rosetta.ObjexxFCL.TypeTraits_unsigned_short_t static method) (pyrosetta.rosetta.std.ios_base method) precompute_all_energies() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) precompute_energies() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) precompute_ig() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) precompute_transforms() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) precompute_unweighted_score() (pyrosetta.rosetta.core.scoring.electron_density_atomwise.ElectronDensityAtomwise method) precomputed_library_mover() (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) PrecomputedFlexbbInteractionGraph (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) PrecomputedFlexbbInteractionGraph.Subsitution (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) PrecomputedLibraryMover (class in pyrosetta.rosetta.protocols.stepwise.modeler.precomputed) PrecomputedPairEnergiesEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) PrecomputedPairEnergiesInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) PrecomputedPairEnergiesNode (class in pyrosetta.rosetta.core.pack.interaction_graph) PRED_DIR (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) pred_ss (pyrosetta.rosetta.core.io.external.PsiPredResult property) PREData (class in pyrosetta.rosetta.core.scoring.nmr.pre) predefine_search() (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) PredesignPerturbMover (class in pyrosetta.rosetta.protocols.enzdes) PredesignPerturbMoverCreator (class in pyrosetta.rosetta.protocols.enzdes) Predicate (class in pyrosetta.rosetta.core.scoring) predicate() (pyrosetta.rosetta.core.scoring.lDDT_Calculator method) predict_ss() (pyrosetta.rosetta.protocols.ss_prediction.SS_predictor method) PredictedBurialEvaluator (class in pyrosetta.rosetta.protocols.simple_filters) PredictedBurialFnEvaluatorCreator (class in pyrosetta.rosetta.protocols.simple_filters) PREDistanceRecord (class in pyrosetta.rosetta.protocols.nmr.pre) PREEnergy (class in pyrosetta.rosetta.protocols.nmr.pre) PREEnergyCreator (class in pyrosetta.rosetta.protocols.nmr.pre) preexisting_positions() (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) pref_ref_use_first_few_decoys (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) pref_use_scud (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) pref_use_sig (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) PREFERENCE_NA (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceType attribute) preference_type (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData property) preferred_contact_angle (pyrosetta.rosetta.protocols.sewing.hashing.IdealContact property) preferred_dihedral_1 (pyrosetta.rosetta.protocols.sewing.hashing.IdealContact property) preferred_dihedral_2 (pyrosetta.rosetta.protocols.sewing.hashing.IdealContact property) preferred_distance (pyrosetta.rosetta.protocols.sewing.hashing.IdealContact property) preferred_properties() (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) PREFERRED_ROOT (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) preferred_root_res() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) prefix() (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.utility.options.OptionCollection static method) prefix_ (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker property) prefix_each_output_pdb() (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) prefix_name() (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry method) preliminary_job_node() (pyrosetta.rosetta.protocols.jd3.standard.StandardInnerLarvalJob method) PreliminaryLarvalJob (class in pyrosetta.rosetta.protocols.jd3.standard) PreliminaryLarvalJobTracker (class in pyrosetta.rosetta.protocols.jd3.standard) preload_motif_data() (in module pyrosetta.rosetta.core.scoring.motif) PreloadedPDB (class in pyrosetta.rosetta.protocols.cluster.calibur) preminimize() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) preminimize_pose() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) PREMover (class in pyrosetta.rosetta.protocols.nmr.pre) PREMoverCreator (class in pyrosetta.rosetta.protocols.nmr.pre) PREMultiSet (class in pyrosetta.rosetta.core.scoring.nmr.pre) prep_for_neighbors_perturbation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) prepack() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) prepack_input_structure() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) PrepackMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) PrepackMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) prepare() (pyrosetta.rosetta.cppdb.backend.connection method) (pyrosetta.rosetta.cppdb.session method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.utility.sql_database.session method) prepare_constraints_energy_container() (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) prepare_enrich_stage() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) prepare_for_altbb_move_to_closest_state() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) prepare_for_altbb_move_to_state() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) prepare_for_FASTER() (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) prepare_for_match_enumeration() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamCoordinateKinemage method) prepare_for_neighbors_substitution() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) prepare_for_output() (pyrosetta.rosetta.utility.tag.XMLSchemaAttribute method) (pyrosetta.rosetta.utility.tag.XMLSchemaComplexType method) (pyrosetta.rosetta.utility.tag.XMLSchemaElement method) (pyrosetta.rosetta.utility.tag.XMLSchemaModelGroup method) (pyrosetta.rosetta.utility.tag.XMLSchemaParticle method) (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) (pyrosetta.rosetta.utility.tag.XMLSchemaTopLevelElement method) prepare_for_output_writing() (pyrosetta.rosetta.protocols.match.output.CloudPDBWriter method) (pyrosetta.rosetta.protocols.match.output.OutputWriter method) (pyrosetta.rosetta.protocols.match.output.PDBWriter method) (pyrosetta.rosetta.protocols.match.output.PoseMatchOutputWriter method) (pyrosetta.rosetta.protocols.match.output.WriteKinemageOutputter method) prepare_for_packing() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) prepare_for_perturbation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) prepare_for_residue_pair() (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) prepare_for_simulated_annealing() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.EdgeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) prepare_from_prior_sampled_sugar_jobs() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) prepare_from_prior_sampled_sugar_jobs_for_chain_break() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) prepare_graph_for_simulated_annealing() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.MultiplexedAnnealableGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.ResidueArrayAnnealingEvaluator method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) prepare_grid() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer method) prepare_hashing_packer_task_() (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) prepare_loop_in_stage3() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) prepare_loop_in_stage4() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) prepare_output() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) prepare_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) prepare_pose_for_sampling() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) prepare_rotamers_for_packing() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) prepare_scoring() (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) prepare_scratch_residue() (in module pyrosetta.rosetta.core.pose.rna) prepare_search_stage() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) prepare_sets_for_packing() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSets method) prepare_silent_struct() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) prepare_stage1() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) prepare_stage2() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) prepare_stage3() (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) prepare_statement() (pyrosetta.rosetta.cppdb.backend.connection method) prepare_statement_no_catch() (in module pyrosetta.rosetta.basic.database) prepare_task_poses() (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) prepare_to_note_hits_for_completed_round() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) PrepareForCentroid (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) PrepareForCentroidCreator (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) PrepareForFullatom (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) PrepareForFullatomCreator (class in pyrosetta.rosetta.protocols.loop_modeling.utilities) prepend_edge() (pyrosetta.rosetta.core.kinematics.FoldTree method) prepend_new_residues() (in module pyrosetta.rosetta.protocols.denovo_design.components) prepend_output_name() (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) prepend_polymer_residue_before_seqpos() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) prepend_res() (pyrosetta.rosetta.core.pose.PDBInfo method) prepend_to_msg() (pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition method) (pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd method) (pyrosetta.rosetta.core.environment.EXCN_Env_Exception method) (pyrosetta.rosetta.core.environment.EXCN_FTSketchGraph method) (pyrosetta.rosetta.core.id.EXCN_AtomNotFound method) (pyrosetta.rosetta.core.kinematics.EXCN_InvalidFoldTree method) (pyrosetta.rosetta.core.pack.task.ResfileReaderException method) (pyrosetta.rosetta.core.scoring.sc.ShapeComplementarityCalculatorException method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.EXCN_InitFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_CalcFailed method) (pyrosetta.rosetta.core.simple_metrics.metrics.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_cdr_undefined_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_grafting_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_invalid_cdr_region_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_json_cdr_detection_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_numbering_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_scs_failed_ method) (pyrosetta.rosetta.protocols.antibody.grafting._AE_unexpected_region_length_ method) (pyrosetta.rosetta.protocols.antibody.grafting.Grafting_Base_Exception method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Heat_Converged method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.EXCN_Pool_Converged method) (pyrosetta.rosetta.protocols.constraint_generator.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.denovo_design.architects.EXCN_PreFilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent method) (pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent method) (pyrosetta.rosetta.protocols.denovo_design.connection.EXCN_ConnectionSetupFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_NothingToFold method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.loophash.EXCN_bbdb_Merge_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_DB_IO_Failed method) (pyrosetta.rosetta.protocols.loophash.EXCN_Invalid_Hashmap method) (pyrosetta.rosetta.protocols.loophash.EXCN_No_Extra_Data_To_Write method) (pyrosetta.rosetta.protocols.loophash.EXCN_Wrong_DB_Format method) (pyrosetta.rosetta.protocols.loops.EXCN_Loop_not_closed method) (pyrosetta.rosetta.protocols.moves.EXCN_Converged method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_AssignmentNotFound method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_FileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_NoesyAssign method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownAtomname method) (pyrosetta.rosetta.protocols.noesy_assign.EXCN_UnknownResonance method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_CalcFailed method) (pyrosetta.rosetta.protocols.simple_filters.EXCN_InitFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FailedBroking method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_FilterFailed method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Input method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_TopologyBroker method) (pyrosetta.rosetta.protocols.topology_broker.EXCN_Unknown method) (pyrosetta.rosetta.utility.excn.BadInput method) (pyrosetta.rosetta.utility.excn.Exception method) (pyrosetta.rosetta.utility.excn.FileNotFound method) (pyrosetta.rosetta.utility.excn.IOError method) (pyrosetta.rosetta.utility.excn.KeyError method) (pyrosetta.rosetta.utility.excn.NullPointerError method) (pyrosetta.rosetta.utility.excn.RangeError method) (pyrosetta.rosetta.utility.excn.RosettaScriptsOptionError method) (pyrosetta.rosetta.utility.excn.UserCorrectableIssue method) (pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS method) PrependMainchainAtom (class in pyrosetta.rosetta.core.chemical) preprocess_data() (pyrosetta.rosetta.core.scoring.ResidualDipolarCoupling method) preprocess_pose() (pyrosetta.rosetta.core.import_pose.pose_stream.ExtendedPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.LazySilentFilePoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.MetaPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PDBPoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.PoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) PreProlineFilter (class in pyrosetta.rosetta.protocols.denovo_design.filters) PreProlineFilterCreator (class in pyrosetta.rosetta.protocols.denovo_design.filters) prerefine_score_ (pyrosetta.rosetta.protocols.electron_density.RefinementResult property) prerelax_ (pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions property) prescoring_filter_exists() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) prescoring_mover_exists() (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) PreSelectedResidRange (class in pyrosetta.rosetta.core.select) preselection_filter_exists() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) preselection_mover_exists() (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) PresenceCommon (class in pyrosetta.rosetta.protocols.constel) preserve_atom_coords() (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) preserve_buried_contacts() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopInfo method) preserve_c_beta() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) preserve_crystinfo() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) preserve_detailed_balance() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) preserve_header() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) PreserveCBeta (class in pyrosetta.rosetta.core.pack.task.operation) PreserveCBetaCreator (class in pyrosetta.rosetta.core.pack.task.operation) PreserveCBetaRLT (class in pyrosetta.rosetta.core.pack.task.operation) PreserveCBetaRLTCreator (class in pyrosetta.rosetta.core.pack.task.operation) presetClass() (pyrosetta.rosetta.protocols.sparta.GDB method) PRESingle (class in pyrosetta.rosetta.core.scoring.nmr.pre) PRESingleSet (class in pyrosetta.rosetta.core.scoring.nmr.pre) pretty() (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) pretty_print() (pyrosetta.rosetta.core.scoring.mm.MMBondAngleLibrary method) (pyrosetta.rosetta.core.scoring.mm.MMBondLengthLibrary method) pretty_print_atomicoor() (in module pyrosetta.rosetta.core.chemical) PREV_Tab (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) prevent_repacking() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation method) PreventChainFromRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) PreventChainFromRepackingOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) PreventRepacking (class in pyrosetta.rosetta.core.pack.task.operation) PreventRepackingCreator (class in pyrosetta.rosetta.core.pack.task.operation) PreventRepackingRLT (class in pyrosetta.rosetta.core.pack.task.operation) PreventRepackingRLTCreator (class in pyrosetta.rosetta.core.pack.task.operation) PreventResiduesFromRepackingOperation (class in pyrosetta.rosetta.protocols.task_operations) PreventResiduesFromRepackingOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) prevFileName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) previous() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListElement method) (pyrosetta.rosetta.utility.graph.EdgeListElement method) previous_child() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) previous_round_geometry_still_matchable() (pyrosetta.rosetta.protocols.match.OccupiedSpaceHash method) previous_sibling() (pyrosetta.rosetta.core.kinematics.tree.Atom method) (pyrosetta.rosetta.core.kinematics.tree.Atom_ method) (pyrosetta.rosetta.core.kinematics.tree.BondedAtom method) (pyrosetta.rosetta.core.kinematics.tree.JumpAtom method) previous_vertex1 (pyrosetta.rosetta.protocols.viewer.GraphicsState property) previous_vertex2 (pyrosetta.rosetta.protocols.viewer.GraphicsState property) previous_width_vector (pyrosetta.rosetta.protocols.viewer.GraphicsState property) previous_working_pack_res() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) PRF_BASIC (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) PRF_MARKDOWN (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverReportFormat attribute) PRIMARY_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) primary_authors() (pyrosetta.rosetta.basic.citation_manager.Citation method) primary_output_index (pyrosetta.rosetta.protocols.jd3.JobOutputIndex property) PrimaryKey (class in pyrosetta.rosetta.basic.database.schema_generator) PrimarySequenceNeighborhoodSelector (class in pyrosetta.rosetta.core.select.residue_selector) PrimarySequenceNeighborhoodSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) principal_angle_degrees() (in module pyrosetta.rosetta.numeric) principal_component() (pyrosetta.rosetta.protocols.features.helixAssembly.HelicalFragment method) principal_components_and_eigenvalues_ndimensions() (in module pyrosetta.rosetta.numeric) PrincipalQuantumNumber_strings() (pyrosetta.rosetta.core.chemical.ElectronConfiguration static method) print() (pyrosetta.rosetta.basic.database.schema_generator.Column method) (pyrosetta.rosetta.basic.database.schema_generator.Constraint method) (pyrosetta.rosetta.basic.database.schema_generator.DbBigInt method) (pyrosetta.rosetta.basic.database.schema_generator.DbDataType method) (pyrosetta.rosetta.basic.database.schema_generator.DbDouble method) (pyrosetta.rosetta.basic.database.schema_generator.DbInteger method) (pyrosetta.rosetta.basic.database.schema_generator.DbReal method) (pyrosetta.rosetta.basic.database.schema_generator.DbText method) (pyrosetta.rosetta.basic.database.schema_generator.DbTextKey method) (pyrosetta.rosetta.basic.database.schema_generator.DbUUID method) (pyrosetta.rosetta.basic.database.schema_generator.ForeignKey method) (pyrosetta.rosetta.basic.database.schema_generator.GreaterThanConstraint method) (pyrosetta.rosetta.basic.database.schema_generator.Index method) (pyrosetta.rosetta.basic.database.schema_generator.PrimaryKey method) (pyrosetta.rosetta.basic.database.schema_generator.Schema method) (pyrosetta.rosetta.basic.database.schema_generator.UniqueConstraint method) Print() (pyrosetta.rosetta.basic.sampling.orientations.Quaternion method) print() (pyrosetta.rosetta.basic.sampling.orientations.QuaternionGrid method) Print() (pyrosetta.rosetta.basic.sampling.orientations.QuatSet method) print() (pyrosetta.rosetta.core.chemical.AtomType method) (pyrosetta.rosetta.core.chemical.Bond method) (pyrosetta.rosetta.core.chemical.Orbital method) (pyrosetta.rosetta.core.io.raw_data.ScoreMap static method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DotSphere method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBNode method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NodeBase method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesNode method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDots method) (pyrosetta.rosetta.core.pack.interaction_graph.RotamerDotsCache method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyNode method) (pyrosetta.rosetta.core.pose.metrics.PoseMetricContainer method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.elec.electrie.ElecAtom method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairData_1_1 method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairData_1_2 method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairData_1_3 method) (pyrosetta.rosetta.core.scoring.etable.etrie.CountPairDataGeneric method) (pyrosetta.rosetta.core.scoring.etable.etrie.EtableAtom method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPair1BC3 static method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairAll static method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairGeneric static method) (pyrosetta.rosetta.core.scoring.etable.etrie.TrieCountPairNone static method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBAtom method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBCountPairFunction static method) (pyrosetta.rosetta.core.scoring.hbonds.hbtrie.HBCPData method) (pyrosetta.rosetta.core.scoring.lkball.lkbtrie.LKBAtom method) (pyrosetta.rosetta.core.scoring.MembraneTopology method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.mm.mmtrie.MMEnergyTableAtom method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.trie.RotamerTrieBase method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode method) (pyrosetta.rosetta.core.scoring.vdwaals.VDWAtom method) (pyrosetta.rosetta.numeric.expression_parser.TokenSet method) (pyrosetta.rosetta.protocols.constel.ChainTerm method) (pyrosetta.rosetta.protocols.constel.ResidueMask method) (pyrosetta.rosetta.protocols.dna.DnaChains method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentLibrary method) (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode method) (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) (pyrosetta.rosetta.protocols.loophash.WorkUnit_LoopHash method) (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.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) (pyrosetta.rosetta.protocols.moves.MoverStatistics method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_bbGauss method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_CombinePose method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_FragInsert method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_KicCloser method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_LoopHash method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_MD method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_NormalMode method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_PartialAbinitio method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_RamaPerturber method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Relax method) (pyrosetta.rosetta.protocols.mpi_refinement.WorkUnit_Sampler method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover.Design method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover.Overlap method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax method) (pyrosetta.rosetta.protocols.relax.WorkUnit_BatchRelax_and_PostRescore method) (pyrosetta.rosetta.protocols.scoring.Interface method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.wum.DatabaseEntryWorkUnit method) (pyrosetta.rosetta.protocols.wum.SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_MoverWrapper method) (pyrosetta.rosetta.protocols.wum.WorkUnit_SilentStructStore method) (pyrosetta.rosetta.protocols.wum.WorkUnit_Wait method) (pyrosetta.rosetta.protocols.wum.WorkUnitBase method) (pyrosetta.rosetta.utility.graph.DirectedNode method) (pyrosetta.rosetta.utility.graph.LowMemNode method) (pyrosetta.rosetta.utility.graph.Node method) print_additional_headers() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) print_additional_info_for_net() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) print_addresses_at_level() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) print_all_bond_lengths() (pyrosetta.rosetta.core.chemical.IdealBondLengthSet method) print_all_info() (pyrosetta.rosetta.protocols.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator method) print_all_nodes() (pyrosetta.rosetta.protocols.jd3.JobGenealogist method) print_all_score_headers() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) print_all_types() (pyrosetta.rosetta.core.chemical.MMAtomTypeSet method) print_allowed_types() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) print_alt_energies() (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbEdge method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbEdge method) print_atom_pair_constraints() (in module pyrosetta.rosetta.core.scoring.constraints) print_atom_pair_energy_table() (in module pyrosetta.toolbox.atom_pair_energy) print_avg_cluster_centroid_dist() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) print_backbone_torsions() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) print_base_centroid_atoms_for_rb_entropy() (in module pyrosetta.rosetta.protocols.recces) print_base_state() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) print_bondangles() (pyrosetta.rosetta.core.chemical.ResidueType method) print_cache() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) print_channel_name (pyrosetta.rosetta.basic.TracerOptions property) print_chis() (in module pyrosetta.rosetta.core.chemical) print_cluster_assignment() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) print_cluster_PDBs() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) print_clusters_silentfile() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) print_comments() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_conformation() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_current_energy() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) print_current_state_assignment() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) print_debug() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) print_definitions() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) print_dofs() (pyrosetta.rosetta.protocols.optimize_weights.WrapperOptEMultifunc method) print_dunbrack02_rotlib() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) print_dunbrack10_rotlib() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) print_entity_history() (pyrosetta.rosetta.protocols.pack_daemon.PackDaemon method) print_error_message() (pyrosetta.rosetta.utility.options.BooleanOption static method) (pyrosetta.rosetta.utility.options.BooleanVectorOption static method) (pyrosetta.rosetta.utility.options.FileOption static method) (pyrosetta.rosetta.utility.options.FileVectorOption static method) (pyrosetta.rosetta.utility.options.IntegerOption static method) (pyrosetta.rosetta.utility.options.IntegerVectorOption static method) (pyrosetta.rosetta.utility.options.Option static method) (pyrosetta.rosetta.utility.options.PathOption static method) (pyrosetta.rosetta.utility.options.PathVectorOption static method) (pyrosetta.rosetta.utility.options.RealOption static method) (pyrosetta.rosetta.utility.options.RealVectorOption static method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption static method) (pyrosetta.rosetta.utility.options.ScalarOption static method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_BooleanOptionKey_bool_t static method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_FileOptionKey_utility_file_FileName_t static method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_IntegerOptionKey_int_t static method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_PathOptionKey_utility_file_PathName_t static method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_RealOptionKey_double_t static method) (pyrosetta.rosetta.utility.options.ScalarOption_T_utility_options_StringOptionKey_std_string_t static method) (pyrosetta.rosetta.utility.options.StringOption static method) (pyrosetta.rosetta.utility.options.StringVectorOption static method) (pyrosetta.rosetta.utility.options.VectorOption static method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t static method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t static method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t static method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t static method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t static method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t static method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t static method) print_fragment() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) print_fragment_index() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) print_fragment_seq() (pyrosetta.rosetta.protocols.frag_picker.FragmentCandidate method) print_generation_statistics() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) print_generators() (in module pyrosetta.rosetta.core.scoring.power_diagram) print_grid_param() (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy_parameters_manager method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_parameters_manager_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_parameters_manager_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_parameters_manager_Ts4 method) print_hbonds() (in module pyrosetta.rosetta.protocols.rna.denovo) print_header() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif static method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostreambase_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) print_headers() (in module pyrosetta.rosetta.protocols.hbnet) print_histogram() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERChiSqMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceBounds method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDistanceDistribution method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJaccardMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERJSMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERMiscMethod method) (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEEROverlapMethod method) print_info() (pyrosetta.rosetta.core.pose.rna.BasePair method) print_information() (in module pyrosetta.rosetta.protocols.rosetta_scripts) print_internal_coords() (in module pyrosetta.rosetta.protocols.rna.denovo) print_internal_energies() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbNode method) print_job_template() (in module pyrosetta.rosetta.protocols.jd3) print_lib_to_file() (pyrosetta.rosetta.protocols.splice.RotLibOut method) print_list_to_string() (in module pyrosetta.rosetta.protocols.hbnet) print_metric() (pyrosetta.rosetta.core.pose.Pose method) print_mut_string() (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info method) print_mutation_data() (pyrosetta.rosetta.protocols.pmut_scan.MutationData method) print_netcharge_and_mutations() (pyrosetta.rosetta.protocols.design_opt.Supercharge method) print_network() (in module pyrosetta.rosetta.protocols.hbnet) print_network_w_pdb_numbering() (in module pyrosetta.rosetta.protocols.hbnet) print_pack_report() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) print_parent_remarks() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_partners() (in module pyrosetta.rosetta.core.scoring.power_diagram) print_peak_info() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) print_point() (in module pyrosetta.rosetta.numeric.kdtree) print_points() (in module pyrosetta.rosetta.numeric.kdtree) print_population() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) print_pretty_path_distances() (pyrosetta.rosetta.core.chemical.ResidueType method) print_probabilities() (in module pyrosetta.rosetta.numeric) print_quantiles() (pyrosetta.rosetta.core.scoring.motif.XformScore method) print_raw_numbers() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) print_relax_report() (pyrosetta.rosetta.protocols.vip.VIP_Mover method) print_report() (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_CompareTotalScore method) (pyrosetta.rosetta.protocols.frag_picker.BoundedCollector_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.CandidatesCollector method) (pyrosetta.rosetta.protocols.frag_picker.GrabAllCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaCollector method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) print_residue_numbers() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_residue_pair_energies() (in module pyrosetta.toolbox.atom_pair_energy) print_residues_near_water() (in module pyrosetta.rosetta.protocols.hydrate) print_roc_curve() (pyrosetta.rosetta.numeric.RocCurve method) print_rot_data() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) print_rot_data_vec() (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) print_rot_vec() (pyrosetta.rosetta.protocols.pose_metric_calculators.RotamerRecovery method) print_score() (pyrosetta.rosetta.protocols.optimize_weights.ConstraintedOptimizationWeightFunc method) (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PSSMOptEPositionData method) print_score_functions() (pyrosetta.rosetta.core.scoring.disulfides.FullatomDisulfidePotential method) print_score_header() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_scores() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.raw_data.RawStruct method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructJSON method) (pyrosetta.rosetta.core.io.raw_data.ScoreStructText method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) (pyrosetta.rosetta.core.scoring.motif.XformScore method) print_scores_norm() (pyrosetta.rosetta.core.scoring.motif.XformScore method) print_sequence_pdb_nums() (in module pyrosetta.rosetta.protocols.dna) print_sequences_pdb_nums() (in module pyrosetta.rosetta.protocols.dna) print_statistics() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) print_string() (pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info method) print_string_to_PDBfile() (pyrosetta.rosetta.protocols.pockets.GenPharmacophore method) print_submotif_info() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RigidBodySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.io.silent.SilentStruct method) print_sugar_pucker_state() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) print_summary() (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.toolbox.ClusterBase method) (pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle method) print_template_script() (in module pyrosetta.rosetta.protocols.rosetta_scripts) print_to_file() (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) print_to_oegrid() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) print_to_pdb() (pyrosetta.rosetta.protocols.pockets.FingerprintBase method) (pyrosetta.rosetta.protocols.pockets.NonPlaidFingerprint method) (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) print_torsion_info() (in module pyrosetta.rosetta.core.pose.rna) (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) print_tree() (in module pyrosetta.rosetta.numeric.kdtree) print_unprocessed_incoming_messages() (pyrosetta.rosetta.utility.SimulateMPI static method) print_unprocessed_outgoing_messages() (pyrosetta.rosetta.utility.SimulateMPI static method) print_vertex_groups() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) print_vertices() (in module pyrosetta.rosetta.core.scoring.power_diagram) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.InteractionGraphBase method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PDInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemoryInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.FlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.OTFFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.PrecomputedFlexbbInteractionGraph method) (pyrosetta.rosetta.protocols.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) (pyrosetta.rosetta.utility.graph.Digraph method) (pyrosetta.rosetta.utility.graph.Graph method) (pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t method) print_water_weight_grid_xz_plane() (pyrosetta.rosetta.core.energy_methods.WaterWeightGridSet method) print_WorkingParameters_info() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) print_xyz() (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) printContent() (pyrosetta.rosetta.protocols.pockets.SmallMol method) printCoordinates() (pyrosetta.rosetta.protocols.pockets.SmallMol method) PrintErrorAndQuit() (pyrosetta.rosetta.protocols.hybridization.TMalign method) PrintEuler() (pyrosetta.rosetta.basic.sampling.orientations.Quaternion method) printflags (pyrosetta.rosetta.numeric.nls.lm_control_struct property) printGrishinFormat() (pyrosetta.rosetta.core.sequence.SequenceAlignment method) priority() (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.protocols.topology_broker.claims.SequenceClaim method) priority_queue_protocols_motif_grafting_movers_MotifMatch_std_vector_protocols_motif_grafting_movers_MotifMatch_std_less_protocols_motif_grafting_movers_MotifMatch_t (class in pyrosetta.rosetta.std) private_data_to_public_array() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) private_index() (pyrosetta.rosetta.utility.keys.AutoKey_utility_options_Option_utility_keys_Key_utility_keys_NoClient_t method) (pyrosetta.rosetta.utility.keys.Key method) (pyrosetta.rosetta.utility.keys.VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) pro_cd_cprev_n_ca_interres_improper_params() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) pro_CD_index() (pyrosetta.rosetta.core.energy_methods.ResidueCartBondedParameters method) pro_close (pyrosetta.rosetta.core.scoring.ScoreType attribute) pro_close_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) prob (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer property) prob() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) prob_ (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_double_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBDepNRChiSample_float_t property) (pyrosetta.rosetta.core.pack.dunbrack.BBIndNRChiSample_float_t property) prob_accum (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer property) prob_level_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) prob_native_amino_acid (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) prob_native_amino_acid_with_unfolded_energy (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) prob_native_ligand_pose (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) prob_native_rotamer (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) prob_native_structure (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) prob_random_pert_current() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) prob_sigmoid_m_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) prob_sigmoid_tau_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) prob_sigmoid_w_ (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignmentParameters property) prob_sum_of_gaussians() (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) prob_uniform() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) prob_withinrot() (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) probA() (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) probabilistically_commit_relaxation() (pyrosetta.rosetta.core.pack.interaction_graph.FASTERInteractionGraph method) probabilities (pyrosetta.rosetta.core.scoring.carbohydrates.CHIDihedralSamplingData property) (pyrosetta.rosetta.core.scoring.carbohydrates.OmegaPreferenceSamplingData property) probability (pyrosetta.rosetta.core.pack.dunbrack.ChiSet property) PROBABILITY (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 attribute) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2.ScoreType attribute) probability (pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBSampleType attribute) probability() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Config method) (pyrosetta.rosetta.protocols.mean_field.AAProb method) (pyrosetta.rosetta.protocols.mean_field.RotProb method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) probability_ (pyrosetta.rosetta.core.pack.dunbrack.ProbSortClass property) probability_limit() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) probability_matrix() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) probability_row() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) probability_to_accumulate_while_building_rotamers() (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_3_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_4_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibrary_5_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_1_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_1_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_2_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_3_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_4_t method) (pyrosetta.rosetta.core.pack.dunbrack.SemiRotamericSingleResidueDunbrackLibrary_2_5_t method) (pyrosetta.rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary method) ProbabilityConservationMetric (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) ProbabilityConservationMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.per_residue_metrics) probabilty_row() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) probB() (pyrosetta.rosetta.core.scoring.packstat.PackingScore method) Probe (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover.StructureOutputMode attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe attribute) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe.StructureOutputMode attribute) probe_radii (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) probe_radius() (pyrosetta.rosetta.protocols.match.BumpGrid static method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) probe_radius_for_atom_type() (in module pyrosetta.rosetta.protocols.match) ProbeRadius (class in pyrosetta.rosetta.protocols.match) probit() (in module pyrosetta.rosetta.core.scoring.epr_deer) ProbSortClass (class in pyrosetta.rosetta.core.pack.dunbrack) proceed() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) process() (in module pyrosetta.rosetta.basic.options) (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) process_data() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.MatchConstraintFileInfo method) process_deallocation_message() (pyrosetta.rosetta.protocols.jd3.chunk_library.ChunkLibraryJobQueen method) (pyrosetta.rosetta.protocols.jd3.full_model.FullModelJobQueen method) (pyrosetta.rosetta.protocols.jd3.JobQueen method) (pyrosetta.rosetta.protocols.jd3.standard.StandardJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueen method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker method) (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsJobQueen method) process_decoy() (in module pyrosetta.rosetta.protocols.features.strand_assembly) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) process_deletions() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) process_entire_pose() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) process_hit() (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatchUpstreamResProcessor method) (pyrosetta.rosetta.protocols.match.output.PoseInserter method) (pyrosetta.rosetta.protocols.match.output.UpstreamHitCacher method) (pyrosetta.rosetta.protocols.match.output.WriteUpstreamHitKinemage method) (pyrosetta.rosetta.protocols.match.upstream.UpstreamResidueProcessor method) process_input_file() (in module pyrosetta.rosetta.core.import_pose) process_insertions() (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) process_line() (in module pyrosetta.rosetta.protocols.ligand_docking) process_match() (pyrosetta.rosetta.protocols.match.output.MatchConsolidator method) (pyrosetta.rosetta.protocols.match.output.MatchOutputter method) (pyrosetta.rosetta.protocols.match.output.MatchProcessor method) process_matches() (pyrosetta.rosetta.protocols.match.Matcher method) process_motifs() (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) process_pdb_header() (pyrosetta.rosetta.protocols.forge.remodel.RemodelEnzdesCstModule method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO method) process_score() (pyrosetta.rosetta.protocols.optimize_weights.DDGBindOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.DDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermDDGMutationOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.NestedEnergyTermPNatAAOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatLigPoseOptEData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatStructureOptEData method) process_symmdef_file() (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) processed() (pyrosetta.rosetta.utility.SimulateMPIMessage method) ProcessorFactory (class in pyrosetta.rosetta.protocols.match.output) ProClosureEnergy (class in pyrosetta.rosetta.core.energy_methods) ProClosureEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) PRODUCT (pyrosetta.rosetta.protocols.calc_taskop_filters.Operation attribute) product() (in module pyrosetta.rosetta.core.pack.dunbrack) (in module pyrosetta.rosetta.numeric) prof_reset() (in module pyrosetta.rosetta.basic) prof_row() (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.protocols.frag_picker.LAMBEGO_IO method) (pyrosetta.rosetta.protocols.frag_picker.TorsionBinIO method) prof_show() (in module pyrosetta.rosetta.basic) prof_start_function_body() (in module pyrosetta.rosetta.basic) prof_stop_function_body() (in module pyrosetta.rosetta.basic) profile() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.sequence.ChemicalShiftSequence method) (pyrosetta.rosetta.core.sequence.SequenceCoupling method) (pyrosetta.rosetta.core.sequence.SequenceProfile method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) profile_config() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) profile_mapping() (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) profile_struct() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) profile_weight_away_from_interface() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) ProfilerMover (class in pyrosetta.rosetta.protocols.moves) ProfileScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreBlosum62 (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreDistWeight (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreL1 (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreStructL1 (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileScoreSubMatrix (class in pyrosetta.rosetta.protocols.frag_picker.scores) ProfileThis (class in pyrosetta.rosetta.basic) ProfSimScoringScheme (class in pyrosetta.rosetta.core.sequence) ProfTag (class in pyrosetta.rosetta.basic) ProgressBarObserver (class in pyrosetta.rosetta.protocols.canonical_sampling) ProgressBarObserverCreator (class in pyrosetta.rosetta.protocols.canonical_sampling) prohibit_property_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) prohibit_property_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) prohibit_res_identity_i() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) prohibit_res_identity_iplus1() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) prohibit_single_residue_loops() (pyrosetta.rosetta.protocols.loops.LoopFromFileData method) ProhibitResidueProperties (class in pyrosetta.rosetta.core.pack.task.operation) ProhibitResiduePropertiesCreator (class in pyrosetta.rosetta.core.pack.task.operation) ProhibitSpecifiedBaseResidueTypes (class in pyrosetta.rosetta.core.pack.task.operation) ProhibitSpecifiedBaseResidueTypesCreator (class in pyrosetta.rosetta.core.pack.task.operation) project_deltaE_for_substitution() (pyrosetta.rosetta.core.pack.interaction_graph.DensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTERNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyNode method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.PDNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistNode method) (pyrosetta.rosetta.protocols.flexpack.interaction_graph.MinimalistFlexbbNode method) project_normal() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) project_parallel() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) project_ZYX_euler_on_cart() (in module pyrosetta.rosetta.core.kinematics.jacobian) projected_normal() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) projected_parallel() (pyrosetta.rosetta.core.scoring.sc.Atom method) (pyrosetta.rosetta.numeric.xyzTriple_unsigned_long_t method) (pyrosetta.rosetta.numeric.xyzVector_double_t method) (pyrosetta.rosetta.numeric.xyzVector_float_t method) (pyrosetta.rosetta.numeric.xyzVector_int_t method) (pyrosetta.rosetta.numeric.xyzVector_unsigned_long_t method) projection_area() (in module pyrosetta.rosetta.numeric.geometry) projection_matrix() (in module pyrosetta.rosetta.numeric) projperp() (in module pyrosetta.rosetta.protocols.sic_dock) proline_N_is_lk_nonpolar (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) ProlineFixMover (class in pyrosetta.rosetta.protocols.simple_moves) ProlinePhiScore (class in pyrosetta.rosetta.protocols.frag_picker.scores) promote_sameresidue_child_of_jump_atom() (in module pyrosetta.rosetta.core.conformation) promote_sameresidue_nonjump_child() (pyrosetta.rosetta.core.kinematics.AtomTree method) propagate_best_from_previous_generation() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) PropagateClashCheckFilter (class in pyrosetta.rosetta.protocols.dna_dock) PropagateClashCheckFilterCreator (class in pyrosetta.rosetta.protocols.dna_dock) PROPARGYL_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) propeller() (pyrosetta.rosetta.protocols.dna.DNABasepair method) properties (pyrosetta.rosetta.cppdb.connection_info property) properties() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) (pyrosetta.rosetta.core.chemical.ResidueTypeFinder method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo method) properties_match_this() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet method) PROPERTY (class in pyrosetta.rosetta.core.pack.task) property() (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabel method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabel method) property_ (pyrosetta.rosetta.core.pack.task.PROPERTY property) property_from_string() (pyrosetta.rosetta.core.chemical.AtomPropertiesManager static method) property_penalty() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) property_set_indices_matching_residue() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) proposal_density() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover method) proposal_density_ratio() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) proposal_probability() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) proposed_one_body_energy() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleNode method) proposed_since_last_batch() (pyrosetta.rosetta.protocols.abinitio.HedgeArchive method) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax method) (pyrosetta.rosetta.protocols.abinitio.IterativeBase method) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid method) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) props() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) ProQ (pyrosetta.rosetta.core.scoring.ScoreType attribute) ProQ_Energy (class in pyrosetta.rosetta.core.energy_methods) ProQ_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) ProQM (pyrosetta.rosetta.core.scoring.ScoreType attribute) ProQPotential (class in pyrosetta.rosetta.core.scoring) ProtectedConformation (class in pyrosetta.rosetta.protocols.environment) PROTEIN (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid attribute) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid.PtType attribute) protein_atom (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) protein_atom_charge (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) protein_atom_coords (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) protein_atom_id (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) protein_atom_name_to_num() (in module pyrosetta.rosetta.core.scoring.rna) protein_atom_type (pyrosetta.rosetta.protocols.ligand_docking.rdf.AtomPairData property) PROTEIN_ATR_REP (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) PROTEIN_BETA_ANTIPARALLEL (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) PROTEIN_CCD_CLOSURE (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) protein_dielectric() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) protein_dna_motif() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) protein_DNA_motif_build_positions_JA() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) protein_DNA_motif_target_positions_JA() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) protein_family() (pyrosetta.rosetta.protocols.splice.Splice method) protein_file_name_ (pyrosetta.rosetta.protocols.cluster.calibur.SimPDB property) PROTEIN_FRAGMENT (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) protein_interface_design() (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) PROTEIN_MAIN_CHAIN (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType attribute) protein_neighbors() (pyrosetta.rosetta.protocols.dna.DnaInterfaceFinder method) protein_pack_all() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) protein_packing() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) protein_packing_distance() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_MinimizerOptions method) protein_positions() (pyrosetta.rosetta.protocols.motifs.LigandMotifSearch method) (pyrosetta.rosetta.protocols.motifs.MotifSearch method) protein_prepack() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) protein_residue() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer method) protein_rot() (pyrosetta.rosetta.protocols.simple_moves.WaterRotsDB method) protein_slice_diameter() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) protein_torsion_end (pyrosetta.rosetta.core.scoring.ProteinTorsion attribute) ProteinAtrRepChecker (class in pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker) ProteinAtrRepScreener (class in pyrosetta.rosetta.protocols.stepwise.legacy.screener) ProteinBackboneAtomAtomPairFeatures (class in pyrosetta.rosetta.protocols.features) ProteinBackboneAtomAtomPairFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinBackboneBuildPoint (class in pyrosetta.rosetta.protocols.match.upstream) ProteinBackboneTorsionAngleFeatures (class in pyrosetta.rosetta.protocols.features) ProteinBackboneTorsionAngleFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinBetaAntiParallelStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.protein) ProteinBondGeometryFeatures (class in pyrosetta.rosetta.protocols.features) ProteinBondGeometryFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinCCD_ClosureScreener (class in pyrosetta.rosetta.protocols.stepwise.screener) ProteinCore (class in pyrosetta.rosetta.protocols.task_operations) ProteinCoreFilterCreator (class in pyrosetta.rosetta.protocols.task_operations) ProteinFragmentStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.protein) ProteinInterfaceDesignOperation (class in pyrosetta.rosetta.protocols.task_operations) ProteinInterfaceDesignOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) ProteinInterfaceMultiStateDesignMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) ProteinInterfaceMultiStateDesignMoverCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) ProteinLigandInterfaceUpweighter (class in pyrosetta.rosetta.protocols.enzdes) ProteinLigandInterfaceUpweighterOperationCreator (class in pyrosetta.rosetta.protocols.enzdes) ProteinMainChainStepWiseSampler (class in pyrosetta.rosetta.protocols.stepwise.sampler.protein) ProteinMPNNMover (class in pyrosetta.rosetta.protocols.protein_mpnn) ProteinMPNNMoverCreator (class in pyrosetta.rosetta.protocols.protein_mpnn) ProteinMPNNProbabilitiesMetric (class in pyrosetta.rosetta.protocols.protein_mpnn) ProteinMPNNProbabilitiesMetricCreator (class in pyrosetta.rosetta.protocols.protein_mpnn) ProteinProteinInterfaceUpweighter (class in pyrosetta.rosetta.protocols.pack_interface) ProteinProteinInterfaceUpweighterTaskOperationCreator (class in pyrosetta.rosetta.protocols.pack_interface) ProteinResidueConformationFeatures (class in pyrosetta.rosetta.protocols.features) ProteinResidueConformationFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinResidueSelector (class in pyrosetta.rosetta.protocols.fold_from_loops.selectors) ProteinResidueSelectorCreator (class in pyrosetta.rosetta.protocols.fold_from_loops.selectors) ProteinRMSDFeatures (class in pyrosetta.rosetta.protocols.features) ProteinRMSDFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinRMSDNoSuperpositionFeatures (class in pyrosetta.rosetta.protocols.features) ProteinRMSDNoSuperpositionFeaturesCreator (class in pyrosetta.rosetta.protocols.features) ProteinSCSampler (class in pyrosetta.rosetta.protocols.match.upstream) ProteinSilentReport (class in pyrosetta.rosetta.protocols.features) ProteinSilentStruct_SinglePrecCreator (class in pyrosetta.rosetta.core.io.silent) ProteinSilentStructCreator (class in pyrosetta.rosetta.core.io.silent) ProteinTorsion (class in pyrosetta.rosetta.core.scoring) ProteinUpstreamBuilder (class in pyrosetta.rosetta.protocols.match.upstream) ProtLigEnsemble (class in pyrosetta.rosetta.protocols.ligand_docking) ProtLigEnsembleCreator (class in pyrosetta.rosetta.protocols.ligand_docking) ProtLigPair_info (class in pyrosetta.rosetta.protocols.ligand_docking) proto_h4 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) proto_l4 (pyrosetta.rosetta.protocols.antibody.CDRNameEnum attribute) Protocol (class in pyrosetta.rosetta.protocols.abinitio) protocol_option_set() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) ProtocolFeatures (class in pyrosetta.rosetta.protocols.features) protocols() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJob method) PROTOCOLS_GENERIC (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel attribute) PROTOCOLS_JOB_DISTRIBUTOR (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel attribute) PROTOCOLS_MINIMIZATION_PACKING (pyrosetta.rosetta.basic.thread_manager.RosettaThreadRequestOriginatingLevel attribute) ProtocolSettingsMetric (class in pyrosetta.rosetta.core.simple_metrics.composite_metrics) ProtocolSettingsMetricCreator (class in pyrosetta.rosetta.core.simple_metrics.composite_metrics) proton() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) proton_chi_2_chi() (pyrosetta.rosetta.core.chemical.ResidueType method) proton_chi_extra_samples() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.ResidueType method) proton_chi_extra_samples_for_chi() (pyrosetta.rosetta.core.chemical.MutableResidueType method) proton_chi_samples() (pyrosetta.rosetta.core.chemical.MutableChiRecord method) (pyrosetta.rosetta.core.chemical.ResidueType method) proton_chi_samples_for_chi() (pyrosetta.rosetta.core.chemical.MutableResidueType method) proton_index() (pyrosetta.rosetta.protocols.noesy_assign.MethylNames method) proton_indices() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup method) proton_tolerance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) PROTONATED (pyrosetta.rosetta.core.chemical.VariantType attribute) protonated_H1_adenosine_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) PROTONATED_N1 (pyrosetta.rosetta.core.chemical.VariantType attribute) PROTONATED_N3 (pyrosetta.rosetta.core.chemical.VariantType attribute) ProtonResonance (class in pyrosetta.rosetta.protocols.noesy_assign) provide_attributes() (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops static method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors static method) provide_attributes_and_subelements() (pyrosetta.rosetta.protocols.fldsgn.MatchResidues static method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover static method) provide_citation_info() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette method) (pyrosetta.rosetta.core.pack.palette.PackerPalette method) (pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG method) (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.core.pack.task.operation.ReplicateTask method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAAS method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperation method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLT method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplings method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinks method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperation method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealer method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.DockingScoreFunction method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictor method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopePredictorSVM method) (pyrosetta.rosetta.core.scoring.MinScoreScoreFunction method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.ScoreFunction method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelector method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelector method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.CompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.PerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.RealMetric method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetric method) (pyrosetta.rosetta.core.simple_metrics.StringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) (pyrosetta.rosetta.protocols.abinitio.AbrelaxMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptStageMover method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM method) (pyrosetta.rosetta.protocols.abinitio.abscript.StagePreparer method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM method) (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper method) (pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl method) (pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) (pyrosetta.rosetta.protocols.abinitio.Protocol method) (pyrosetta.rosetta.protocols.abinitio.ResolutionSwitcher method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover method) (pyrosetta.rosetta.protocols.analysis.PackStatMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredPerturbMover method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredRefineMover method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter method) (pyrosetta.rosetta.protocols.antibody.AntibodyModelerProtocol method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover method) (pyrosetta.rosetta.protocols.antibody.CDRsMinPackMin method) (pyrosetta.rosetta.protocols.antibody.CloseOneCDRLoop 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.MutateFrameworkForCluster method) (pyrosetta.rosetta.protocols.antibody.design.ResnumFromStringsWithRangesSelector method) (pyrosetta.rosetta.protocols.antibody.GraftCDRLoopsProtocol method) (pyrosetta.rosetta.protocols.antibody.GraftedStemOptimizer method) (pyrosetta.rosetta.protocols.antibody.GraftOneCDRLoop method) (pyrosetta.rosetta.protocols.antibody.H3CterInsert method) (pyrosetta.rosetta.protocols.antibody.H3PerturbCCD method) (pyrosetta.rosetta.protocols.antibody.H3RefineCCD method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRamp method) (pyrosetta.rosetta.protocols.antibody.LHRepulsiveRampLegacy method) (pyrosetta.rosetta.protocols.antibody.LHSnugFitLegacy method) (pyrosetta.rosetta.protocols.antibody.RefineBetaBarrel method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockProtocol method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors method) (pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) (pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftMover method) (pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover method) (pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro method) (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.DesignRepackMover method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy method) (pyrosetta.rosetta.protocols.canonical_sampling.CanonicalSamplingMover method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover method) (pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver method) (pyrosetta.rosetta.protocols.canonical_sampling.WTEBiasEnergy method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover method) (pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover method) (pyrosetta.rosetta.protocols.contact_map.ContactMap method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol method) (pyrosetta.rosetta.protocols.cryst.CrystRMS method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Metal_HelperBase method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.OctahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.One_Four_BBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.SquarePyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TBMB_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TetrahedralMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.Thioether_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TMA_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPlanarMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker.TrigonalPyramidalMetal_Helper method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations method) (pyrosetta.rosetta.protocols.ddg.ddGMover method) (pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter 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.ExtendChainMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetPoseSecstructFromStructureDataMover method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.Supercharge method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplings method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilter method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilter method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover method) (pyrosetta.rosetta.protocols.docking.DockingEnsemblePrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingHighRes method) (pyrosetta.rosetta.protocols.docking.DockingHighResFilter method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation method) (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) (pyrosetta.rosetta.protocols.docking.DockingLowResFilter method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol method) (pyrosetta.rosetta.protocols.docking.DockingProtocol method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.DockMCMCycle method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol method) (pyrosetta.rosetta.protocols.docking.DockMinMover method) (pyrosetta.rosetta.protocols.docking.DockSetupMover method) (pyrosetta.rosetta.protocols.docking.EllipsoidalRandomizationMover method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover method) (pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.docking.InterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMover method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparately method) (pyrosetta.rosetta.protocols.docking.SidechainMinMover method) (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol method) (pyrosetta.rosetta.protocols.docking.TemperedDocking method) (pyrosetta.rosetta.protocols.domain_assembly.AddAssemblyConstraints method) (pyrosetta.rosetta.protocols.domain_assembly.AssembleLinkerMover method) (pyrosetta.rosetta.protocols.domain_assembly.CombineChainsMover method) (pyrosetta.rosetta.protocols.domain_assembly.PostDockAssemblyScorer method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentBaseMover method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores method) (pyrosetta.rosetta.protocols.electron_density.DockFragmentsIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.DockPDBIntoDensityMover method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover method) (pyrosetta.rosetta.protocols.environment.claims.EnvLabelSelector method) (pyrosetta.rosetta.protocols.environment.ClientMover method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM method) (pyrosetta.rosetta.protocols.environment.EnvMover method) (pyrosetta.rosetta.protocols.environment.ScriptCM method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs method) (pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter method) (pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter method) (pyrosetta.rosetta.protocols.enzdes.MinimizeStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.RepackLigandSiteWithoutLigandMover method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter method) (pyrosetta.rosetta.protocols.enzdes.SecondaryMatchProtocol method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.EnzymaticMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover method) (pyrosetta.rosetta.protocols.features.ReportToDB method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB method) (pyrosetta.rosetta.protocols.fibril.SetupForFibrilMover method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter method) (pyrosetta.rosetta.protocols.filters.CombinedFilter method) (pyrosetta.rosetta.protocols.filters.CompoundFilter method) (pyrosetta.rosetta.protocols.filters.ContingentFilter method) (pyrosetta.rosetta.protocols.filters.FalseFilter method) (pyrosetta.rosetta.protocols.filters.Filter method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric method) (pyrosetta.rosetta.protocols.filters.IfThenFilter method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter method) (pyrosetta.rosetta.protocols.filters.StochasticFilter method) (pyrosetta.rosetta.protocols.filters.TimeFilter method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter method) (pyrosetta.rosetta.protocols.filters.TrueFilter method) (pyrosetta.rosetta.protocols.filters.VectorPoseFilter method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.flexpack.FlexPacker method) (pyrosetta.rosetta.protocols.flexpack.OtherContextScoreFunction method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingAbInitio method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingLowRes method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol method) (pyrosetta.rosetta.protocols.floppy_tail.FloppyTailMover method) (pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelector method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelector method) (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelAccumulator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelGlobalFrame method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLigandHandler method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingHighResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingLowResRefinement method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) (pyrosetta.rosetta.protocols.grafting.GraftMoverBase 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.hbnet.ConstrainHBondNetwork method) (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix method) (pyrosetta.rosetta.protocols.hotspot_hashing.AddSearchPatternRotSetOp method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceProbeMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler method) (pyrosetta.rosetta.protocols.hybridization.CartesianHybridize method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler method) (pyrosetta.rosetta.protocols.hybridization.ChunkTrialMover method) (pyrosetta.rosetta.protocols.hybridization.DomainAssembly method) (pyrosetta.rosetta.protocols.hybridization.FoldTreeHybridize method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol method) (pyrosetta.rosetta.protocols.hybridization.InsertChunkMover method) (pyrosetta.rosetta.protocols.hybridization.MRMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentSmoothTrialMover method) (pyrosetta.rosetta.protocols.hybridization.WeightedFragmentTrialMover method) (pyrosetta.rosetta.protocols.hydrate.Hydrate method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers method) (pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom method) (pyrosetta.rosetta.protocols.ligand_docking.TetherLigand method) (pyrosetta.rosetta.protocols.ligand_docking.Transform method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble method) (pyrosetta.rosetta.protocols.ligand_docking.Translate method) (pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile method) (pyrosetta.rosetta.protocols.loop_build.LoopBuildMover method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension method) (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loop_grower.SheetSampler method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder method) (pyrosetta.rosetta.protocols.loop_modeling.LoopMover 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.AcceptanceCheck method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopFilter method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.LoopMoverGroup method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom method) (pyrosetta.rosetta.protocols.loophash.FastGapMover method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibrary method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) (pyrosetta.rosetta.protocols.loophash.LoopHashRelaxProtocol method) (pyrosetta.rosetta.protocols.loophash.Mover_LoopHashRefine method) (pyrosetta.rosetta.protocols.LoopRebuild method) (pyrosetta.rosetta.protocols.LoopRefine method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicWrapper method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopMover method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC 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.loops.loop_mover.refine.LoopMover_Refine_Backrub method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycle method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial method) (pyrosetta.rosetta.protocols.magnesium.MgHydrater method) (pyrosetta.rosetta.protocols.magnesium.MgMinimizer method) (pyrosetta.rosetta.protocols.magnesium.MgMonteCarlo method) (pyrosetta.rosetta.protocols.magnesium.MgOrbitalFrameFinder method) (pyrosetta.rosetta.protocols.magnesium.MgScanner method) (pyrosetta.rosetta.protocols.magnesium.MgWaterHydrogenPacker method) (pyrosetta.rosetta.protocols.make_rot_lib.MakeRotLibMover method) (pyrosetta.rosetta.protocols.match.MatcherMover method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover method) (pyrosetta.rosetta.protocols.matdes.SymDofMover method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover method) (pyrosetta.rosetta.protocols.medal.MedalExchangeMover method) (pyrosetta.rosetta.protocols.medal.MedalMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles method) (pyrosetta.rosetta.protocols.membrane.FlipMover method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequence method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMover method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionRotationMover method) (pyrosetta.rosetta.protocols.membrane.RandomPositionTranslationMover method) (pyrosetta.rosetta.protocols.membrane.RotationMover method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.membrane.SetMembraneCenterMover method) (pyrosetta.rosetta.protocols.membrane.SetMembraneNormalMover method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMover method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TiltMover method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover method) (pyrosetta.rosetta.protocols.membrane.TranslationMover method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover method) (pyrosetta.rosetta.protocols.metal_interface.ZincHeterodimerMover method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.GreenPacker method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerizeMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker method) (pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover method) (pyrosetta.rosetta.protocols.moves.CompositionMover method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.CyclicMover method) (pyrosetta.rosetta.protocols.moves.DsspMover method) (pyrosetta.rosetta.protocols.moves.FilterMover method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover method) (pyrosetta.rosetta.protocols.moves.FilterReporterMover method) (pyrosetta.rosetta.protocols.moves.IfMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.moves.JumpOutMover method) (pyrosetta.rosetta.protocols.moves.MCShowMover method) (pyrosetta.rosetta.protocols.moves.MonteCarloUtil method) (pyrosetta.rosetta.protocols.moves.MoveMapMover method) (pyrosetta.rosetta.protocols.moves.Mover method) (pyrosetta.rosetta.protocols.moves.MoverApplyingMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.MoverForPoseList method) (pyrosetta.rosetta.protocols.moves.NullMover method) (pyrosetta.rosetta.protocols.moves.PDBDumpMover method) (pyrosetta.rosetta.protocols.moves.ProfilerMover method) (pyrosetta.rosetta.protocols.moves.PyMOLMover method) (pyrosetta.rosetta.protocols.moves.RampingMover method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.RepeatMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.StructureRestrictor method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.moves.TrialMover method) (pyrosetta.rosetta.protocols.moves.VectorPoseMover method) (pyrosetta.rosetta.protocols.moves.WhileMover method) (pyrosetta.rosetta.protocols.mpi_refinement.StructAvrgMover method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinder method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover method) (pyrosetta.rosetta.protocols.network.UIMover method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover 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.DisulfideMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot 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.PlacementAuctionMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.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.SecretionOptimizationMover 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.SetupHotspotConstraintsLoopsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover 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.TryRotamers method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) (pyrosetta.rosetta.protocols.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) (pyrosetta.rosetta.protocols.rbsegment_relax.AutoRBMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.GaussianRBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.HelicalGaussianMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.RBSegmentRelax method) (pyrosetta.rosetta.protocols.rbsegment_relax.SequenceShiftMover method) (pyrosetta.rosetta.protocols.rbsegment_relax.StrandTwistingMover method) (pyrosetta.rosetta.protocols.RBSegmentRelaxImpl method) (pyrosetta.rosetta.protocols.recces.RECCES_Mover method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Any method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Comb method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Loop method) (pyrosetta.rosetta.protocols.recces.sampler.MC_OneTorsion method) (pyrosetta.rosetta.protocols.recces.sampler.MC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_MultiSuite method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_OneJump method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Sugar method) (pyrosetta.rosetta.protocols.recces.sampler.rna.MC_RNA_Suite method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter method) (pyrosetta.rosetta.protocols.recon_design.MSDMover method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) (pyrosetta.rosetta.protocols.relax.CentroidRelax method) (pyrosetta.rosetta.protocols.relax.ClassicRelax method) (pyrosetta.rosetta.protocols.relax.FastRelax method) (pyrosetta.rosetta.protocols.relax.LocalRelax method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.MiniRelax method) (pyrosetta.rosetta.protocols.relax.RangeRelaxMover method) (pyrosetta.rosetta.protocols.relax.RelaxProtocolBase method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector method) (pyrosetta.rosetta.protocols.rigid.MembraneCenterPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MembraneNormalPerturbationMover method) (pyrosetta.rosetta.protocols.rigid.MovePoseToMembraneCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDeterministicSpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofRandomTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofSeqTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyDofTransMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbRandomJumpMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodySpinMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) (pyrosetta.rosetta.protocols.rigid.RollMover method) (pyrosetta.rosetta.protocols.rigid.RotateJumpAxisMover method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover method) (pyrosetta.rosetta.protocols.rigid.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyRotationMover method) (pyrosetta.rosetta.protocols.rigid.WholeBodyTranslationMover method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.CoarseRNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.MultipleDomainMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_FragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_HelixMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Minimizer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_Relaxer method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNP_HighResMover method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_FragmentMonteCarlo method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DeNovoOptimizer method) (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMover method) (pyrosetta.rosetta.protocols.rna.setup.RNA_CSA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_JobDistributor method) (pyrosetta.rosetta.protocols.rna.setup.RNA_MonteCarloJobDistributor method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover method) (pyrosetta.rosetta.protocols.RotamerDump.RotamerDumpMover method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter method) (pyrosetta.rosetta.protocols.simple_filters.AbinitioBaseFilter method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.COFilter method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter method) (pyrosetta.rosetta.protocols.simple_filters.DomainInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter method) (pyrosetta.rosetta.protocols.simple_filters.EvaluatedTrialMover method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackerNeighborGraphFilter method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter method) (pyrosetta.rosetta.protocols.simple_filters.PDDFScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.RGFilter method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter method) (pyrosetta.rosetta.protocols.simple_filters.SAXSScoreFilter method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) (pyrosetta.rosetta.protocols.simple_filters.SheetFilter method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter method) (pyrosetta.rosetta.protocols.simple_moves.a3b_hbs.A3BHbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.AddCavitiesMover method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins method) (pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) (pyrosetta.rosetta.protocols.simple_moves.chiral.ChiralMover method) (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.CombinePoseMover method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover method) (pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyDofMover method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) (pyrosetta.rosetta.protocols.simple_moves.CyclizationMover method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover method) (pyrosetta.rosetta.protocols.simple_moves.DME_FilterMover method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.hbs.HbsPatcher method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology method) (pyrosetta.rosetta.protocols.simple_moves.MissingDensityToJumpMover method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopDPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPatcher method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckMinusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopPuckPlusMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomPuckMover method) (pyrosetta.rosetta.protocols.simple_moves.oop.OopRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover method) (pyrosetta.rosetta.protocols.simple_moves.PeptideStapleMover method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover method) (pyrosetta.rosetta.protocols.simple_moves.ProlineFixMover method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover method) (pyrosetta.rosetta.protocols.simple_moves.rational_mc.RationalMonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ method) (pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover method) (pyrosetta.rosetta.protocols.simple_moves.ShakeStructureMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover 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.sidechain_moves.SidechainMoverBase method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover method) (pyrosetta.rosetta.protocols.simple_moves.TorsionSetMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerMover method) (pyrosetta.rosetta.protocols.simple_moves.triazolamer.TriazolamerRandomSmallMover method) (pyrosetta.rosetta.protocols.simple_moves.Tumble method) (pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover method) (pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack1 method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack2 method) (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation method) (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.RotLibOut method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) (pyrosetta.rosetta.protocols.splice.SpliceOut method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) (pyrosetta.rosetta.protocols.star.StarAbinitio method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinMinimizer method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein.StepWiseProteinPoseSetup method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSetup method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.SideChainCopier method) (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens.PolarHydrogenPacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.precomputed.PrecomputedLibraryMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_Closer method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinCCD_MultiPoseCloser method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close.StepWiseProteinKIC_LoopBridger method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.StepWiseProteinBackboneSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge.BulgeUnApplyMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime.O2PrimePacker method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarInstantiateMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarVirtualizeMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarJustInTimeInstantiator method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.VirtualSugarSamplerFromStringList method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseConnectionSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseMinimizer method) (pyrosetta.rosetta.protocols.stepwise.modeler.StepWiseModeler method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddOrDeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMasterMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.VaryLoopLengthMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_AddDeleteMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_O2PrimeMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna.RNA_TorsionMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.StepWiseMonteCarlo method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.CopyDofStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueListStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.input_streams.InputStreamStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.jump.JumpStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinBetaAntiParallelStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinFragmentStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.protein.ProteinMainChainStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KIC_Sampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_KinematicCloser method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_NucleosideStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SuiteStepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSampler method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneDOF method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneTorsion method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValue method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerOneValueComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerRingConformer method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSized method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedAny method) (pyrosetta.rosetta.protocols.stepwise.sampler.StepWiseSamplerSizedComb method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover method) (pyrosetta.rosetta.protocols.surface_docking.CentroidRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.FullatomRelaxMover method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceDockingProtocol method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceOrientMover method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking method) (pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover method) (pyrosetta.rosetta.protocols.symmetry.FaSymDockingSlideTogether method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.symmetry.SymDockingInitialPerturbation method) (pyrosetta.rosetta.protocols.symmetry.SymDockingSlideIntoContact method) (pyrosetta.rosetta.protocols.symmetry.SymmetricRMSMover method) (pyrosetta.rosetta.protocols.symmetry.SymShakeStructureMover method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictOperationsBase method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover method) (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.AlignPoseToInvrotTreeMover method) (pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover method) (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) (pyrosetta.rosetta.protocols.unfolded_state_energy_calculator.UnfoldedStateEnergyCalculatorMover method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover method) provide_citation_info_static() (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator static method) provide_pymol_commands_to_show_groups() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) provide_shared_xml_schema_elements() (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric static method) provide_stored_derivatives() (pyrosetta.rosetta.core.optimization.ArmijoLineMinimization method) (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) (pyrosetta.rosetta.core.optimization.LineMinimizationAlgorithm method) (pyrosetta.rosetta.core.optimization.StrongWolfeLineMinimization method) provide_xml_definition() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) provide_xml_schema() (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocator static method) (pyrosetta.rosetta.basic.resource_manager.locator.DatabaseResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocator static method) (pyrosetta.rosetta.basic.resource_manager.locator.FileListResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocator static method) (pyrosetta.rosetta.basic.resource_manager.locator.FileSystemResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocator static method) (pyrosetta.rosetta.basic.resource_manager.locator.NullResourceLocatorCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderCreator method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorCreator method) (pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoader static method) (pyrosetta.rosetta.core.conformation.symmetry.SymmDataLoaderCreator method) (pyrosetta.rosetta.core.fragment.FragmentSetLoader static method) (pyrosetta.rosetta.core.fragment.FragmentSetLoaderCreator method) (pyrosetta.rosetta.core.import_pose.PoseResourceLoader static method) (pyrosetta.rosetta.core.import_pose.PoseResourceLoaderCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetric static method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.PerResidueSapScoreMetricCreator method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetric static method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapScoreMetricCreator method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPalette static method) (pyrosetta.rosetta.core.pack.palette.CustomBaseTypePackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPalette static method) (pyrosetta.rosetta.core.pack.palette.DefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPalette static method) (pyrosetta.rosetta.core.pack.palette.NCAADefaultPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPalette static method) (pyrosetta.rosetta.core.pack.palette.NoDesignPackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteCreator method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLT static method) (pyrosetta.rosetta.core.pack.task.operation.AddBehaviorRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilter static method) (pyrosetta.rosetta.core.pack.task.operation.AllResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilter static method) (pyrosetta.rosetta.core.pack.task.operation.AnyResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSet static method) (pyrosetta.rosetta.core.pack.task.operation.AppendResidueRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamer static method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerCreator method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSet static method) (pyrosetta.rosetta.core.pack.task.operation.AppendRotamerSetCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIs static method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsnt static method) (pyrosetta.rosetta.core.pack.task.operation.ChainIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShell static method) (pyrosetta.rosetta.core.pack.task.operation.ClashBasedRepackShellCreator method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictions static method) (pyrosetta.rosetta.core.pack.task.operation.DesignRestrictionsCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnative static method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeCreator method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLT static method) (pyrosetta.rosetta.core.pack.task.operation.DisallowIfNonnativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealer static method) (pyrosetta.rosetta.core.pack.task.operation.EnableMultiCoolAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealer static method) (pyrosetta.rosetta.core.pack.task.operation.EnableSmartAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoff static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLT static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraChiCutoffRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamers static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGeneric static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericCreator method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLT static method) (pyrosetta.rosetta.core.pack.task.operation.ExtraRotamersGenericRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperation static method) (pyrosetta.rosetta.core.pack.task.operation.FillAUTOTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrent static method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentCreator method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLT static method) (pyrosetta.rosetta.core.pack.task.operation.IncludeCurrentRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandline static method) (pyrosetta.rosetta.core.pack.task.operation.InitializeExtraRotsFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandline static method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromCommandlineCreator method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollection static method) (pyrosetta.rosetta.core.pack.task.operation.InitializeFromOptionCollectionCreator method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetry static method) (pyrosetta.rosetta.core.pack.task.operation.KeepSequenceSymmetryCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfides static method) (pyrosetta.rosetta.core.pack.task.operation.NoRepackDisulfidesCreator method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilter static method) (pyrosetta.rosetta.core.pack.task.operation.NoResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues static method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResiduesCreator method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset static method) (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubsetCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHG static method) (pyrosetta.rosetta.core.pack.task.operation.OptCysHGCreator method) (pyrosetta.rosetta.core.pack.task.operation.OptH static method) (pyrosetta.rosetta.core.pack.task.operation.OptHCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBeta static method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLT static method) (pyrosetta.rosetta.core.pack.task.operation.PreserveCBetaRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepacking static method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLT static method) (pyrosetta.rosetta.core.pack.task.operation.PreventRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResidueProperties static method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypes static method) (pyrosetta.rosetta.core.pack.task.operation.ProhibitSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile static method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents static method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEventsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasProperty static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueHasPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIs static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksProperty static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueLacksPropertyCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Is static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3Isnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueName3IsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIs static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsnt static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBIndexIsntCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabel static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoHasLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabel static method) (pyrosetta.rosetta.core.pack.task.operation.ResiduePDBInfoLacksLabelCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilter static method) (pyrosetta.rosetta.core.pack.task.operation.ResidueTypeFilterCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAAS static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLT static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASExceptNativeRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLT static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictAbsentCanonicalAASRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperation static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictInteractionGraphThreadsOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepacking static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictResidueToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepacking static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLT static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToRepackingRLTCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResidueProperties static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToResiduePropertiesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypes static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictToSpecifiedBaseResidueTypesCreator method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesign static method) (pyrosetta.rosetta.core.pack.task.operation.RestrictYSDesignCreator method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosion static method) (pyrosetta.rosetta.core.pack.task.operation.RotamerExplosionCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplings static method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerCouplingsCreator method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinks static method) (pyrosetta.rosetta.core.pack.task.operation.SetRotamerLinksCreator method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealer static method) (pyrosetta.rosetta.core.pack.task.operation.UseMultiCoolAnnealerCreator method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector static method) (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelector static method) (pyrosetta.rosetta.core.select.jump_selector.AndJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelector static method) (pyrosetta.rosetta.core.select.jump_selector.ExclusivelySharedJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelector static method) (pyrosetta.rosetta.core.select.jump_selector.InterchainJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidue static method) (pyrosetta.rosetta.core.select.jump_selector.JumpForResidueCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelector static method) (pyrosetta.rosetta.core.select.jump_selector.JumpIndexSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelector static method) (pyrosetta.rosetta.core.select.jump_selector.NotJumpSelectorCreator method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelector static method) (pyrosetta.rosetta.core.select.jump_selector.OrJumpSelectorCreator method) (pyrosetta.rosetta.core.select.movemap.MoveMapFactory static method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.AndResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelector static method) (pyrosetta.rosetta.core.select.residue_selector.AsymmetricUnitSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelector static method) (pyrosetta.rosetta.core.select.residue_selector.BFactorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BinSelector static method) (pyrosetta.rosetta.core.select.residue_selector.BinSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelector static method) (pyrosetta.rosetta.core.select.residue_selector.BlockSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.BondedResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ChainSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.CloseContactResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ConfluentSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.DensityFitResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.FalseResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelector static method) (pyrosetta.rosetta.core.select.residue_selector.FractionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelector static method) (pyrosetta.rosetta.core.select.residue_selector.GlycanLayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelector static method) (pyrosetta.rosetta.core.select.residue_selector.GlycanPositionSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.GlycanResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelector static method) (pyrosetta.rosetta.core.select.residue_selector.GlycanSequonsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector static method) (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelector static method) (pyrosetta.rosetta.core.select.residue_selector.JumpDownstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelector static method) (pyrosetta.rosetta.core.select.residue_selector.JumpUpstreamSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelector static method) (pyrosetta.rosetta.core.select.residue_selector.LayerSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.LogicResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.NeighborhoodResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.NotResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelector static method) (pyrosetta.rosetta.core.select.residue_selector.NumNeighborsSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.OrResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelector static method) (pyrosetta.rosetta.core.select.residue_selector.PhiSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelector static method) (pyrosetta.rosetta.core.select.residue_selector.PrimarySequenceNeighborhoodSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelector static method) (pyrosetta.rosetta.core.select.residue_selector.RandomGlycanFoliageSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.RandomResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueIndexSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInMembraneSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueInSequenceMotifSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueNameSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePDBInfoHasLabelSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResiduePropertySelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSpanSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.ReturnResidueSubsetSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelector static method) (pyrosetta.rosetta.core.select.residue_selector.ScoreTermValueBasedSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SecondaryStructureSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SimpleMetricSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SliceResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SSElementSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.SymmetricalResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.TrueResidueSelectorCreator method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelector static method) (pyrosetta.rosetta.core.select.residue_selector.VirtualResidueSelectorCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.CompositeEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticComplementarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ElectrostaticSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetric static method) (pyrosetta.rosetta.core.simple_metrics.composite_metrics.ProtocolSettingsMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.AverageProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.CalculatorMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomRealValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.CustomStringValueMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.DihedralDistanceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.InteractionEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.ResidueSummaryMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.RMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SecondaryStructureMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResidueCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SelectedResiduesPyMOLMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.ShapeSimilarityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.TimingProfileMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.metrics.TotalEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.HbondMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.LoadedProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueClashMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueDensityFitMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueEnergyMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueGlycanLayerMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueRMSDMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.PerResidueSasaMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.SidechainNeighborCountMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric static method) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestCompositeStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueProbabilitiesMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestPerResidueStringMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestRealMetricCreator method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetric static method) (pyrosetta.rosetta.core.simple_metrics.TestStringMetricCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddCompositionConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddHelixSequenceConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddMHCEpitopeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMover static method) (pyrosetta.rosetta.protocols.aa_composition.AddNetChargeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMover static method) (pyrosetta.rosetta.protocols.aa_composition.ClearCompositionConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptLoopCloserCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMover static method) (pyrosetta.rosetta.protocols.abinitio.abscript.AbscriptMoverCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparer static method) (pyrosetta.rosetta.protocols.abinitio.abscript.ConstraintPreparerCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.FragmentJumpCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.RigidChunkCMCreator method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCM static method) (pyrosetta.rosetta.protocols.abinitio.abscript.StructPerturberCMCreator method) (pyrosetta.rosetta.protocols.abinitio.DomainAssembly static method) (pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetric static method) (pyrosetta.rosetta.protocols.analysis.burial_metrics.PolarGroupBurialPyMolStringMetricCreator method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMover static method) (pyrosetta.rosetta.protocols.analysis.GlycanInfoMoverCreator method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMover static method) (pyrosetta.rosetta.protocols.analysis.InterfaceAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMover static method) (pyrosetta.rosetta.protocols.analysis.LoopAnalyzerMoverCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetric static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.ConstraintsMetricCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMover static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.RunSimpleMetricsMoverCreator method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetric static method) (pyrosetta.rosetta.protocols.analysis.simple_metrics.SequenceRecoveryMetricCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafter static method) (pyrosetta.rosetta.protocols.antibody.AntibodyCDRGrafterCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures static method) (pyrosetta.rosetta.protocols.antibody.AntibodyFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMover static method) (pyrosetta.rosetta.protocols.antibody.AntibodyNumberingConverterMoverCreator method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures static method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeaturesCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.CDRDihedralConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeEpitopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMover static method) (pyrosetta.rosetta.protocols.antibody.constraints.ParatopeSiteConstraintMoverCreator method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover static method) (pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMoverCreator method) (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForClusterCreator method) (pyrosetta.rosetta.protocols.antibody.design.ResnumFromStringsWithRangesSelector static method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelector static method) (pyrosetta.rosetta.protocols.antibody.residue_selector.AntibodyRegionSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelector static method) (pyrosetta.rosetta.protocols.antibody.residue_selector.CDRResidueSelectorCreator method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDock static method) (pyrosetta.rosetta.protocols.antibody.snugdock.SnugDockCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperation static method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfileSetsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperation static method) (pyrosetta.rosetta.protocols.antibody.task_operations.AddCDRProfilesOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperation static method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableAntibodyRegionOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperation static method) (pyrosetta.rosetta.protocols.antibody.task_operations.DisableCDRsOperationCreator method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighbors static method) (pyrosetta.rosetta.protocols.antibody.task_operations.RestrictToCDRsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMover static method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.LocalBackboneMoverCreator method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPrePro static method) (pyrosetta.rosetta.protocols.backbone_moves.RandomizeBBByRamaPreProCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubMover static method) (pyrosetta.rosetta.protocols.backrub.BackrubMoverCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocol static method) (pyrosetta.rosetta.protocols.backrub.BackrubProtocolCreator method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover static method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMoverCreator method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2 static method) (pyrosetta.rosetta.protocols.buns.BuriedUnsatHbondFilter2Creator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilter static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.ConservedPosMutationFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoids static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.MultipleSigmoidsFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.OperatorFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2 static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight2Creator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeightFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid static method) (pyrosetta.rosetta.protocols.calc_taskop_filters.SigmoidFilterCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ConsensusDesignMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.CreateSequenceMotifMoverCreator method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMover static method) (pyrosetta.rosetta.protocols.calc_taskop_movers.ForceDisulfidesMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange static method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchangeCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.MetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMover static method) (pyrosetta.rosetta.protocols.canonical_sampling.SidechainMetropolisHastingsMoverCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder static method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorderCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering static method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTemperingCreator method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserver static method) (pyrosetta.rosetta.protocols.canonical_sampling.TrialCounterObserverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover static method) (pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler static method) (pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens static method) (pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover static method) (pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover static method) (pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover static method) (pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover static method) (pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMover static method) (pyrosetta.rosetta.protocols.chemically_conjugated_docking.UBQ_GTPaseMoverCreator method) (pyrosetta.rosetta.protocols.chemistries.ChemistryCreator method) (pyrosetta.rosetta.protocols.chemistries.ChemistryLoader static method) (pyrosetta.rosetta.protocols.chemistries.ChemistryLoaderCreator method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistry static method) (pyrosetta.rosetta.protocols.chemistries.PatchChemistryCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreCutoffFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilter static method) (pyrosetta.rosetta.protocols.constraint_filters.ConstraintScoreFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilter static method) (pyrosetta.rosetta.protocols.constraint_filters.SavePoseConstraintToFileFilterCreator method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilter static method) (pyrosetta.rosetta.protocols.constraint_filters.ShowConstraintsFilterCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraints static method) (pyrosetta.rosetta.protocols.constraint_generator.AddConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.AtomPairConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.CoordinateConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.DihedralConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.DistanceConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.HydrogenBondConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.MembraneSpanConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.MetalContactsConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraints static method) (pyrosetta.rosetta.protocols.constraint_generator.RemoveConstraintsCreator method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.ResidueTypeConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGenerator static method) (pyrosetta.rosetta.protocols.constraint_generator.TerminiConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMover static method) (pyrosetta.rosetta.protocols.constraint_movers.AddConstraintsToCurrentConformationMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ClearConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ConstraintSetMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMover static method) (pyrosetta.rosetta.protocols.constraint_movers.CstInfoMoverCreator method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMover static method) (pyrosetta.rosetta.protocols.constraint_movers.ResidueTypeConstraintMoverCreator method) (pyrosetta.rosetta.protocols.contact_map.ContactMap static method) (pyrosetta.rosetta.protocols.contact_map.ContactMapCreator method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocol static method) (pyrosetta.rosetta.protocols.coupled_moves.CoupledMovesProtocolCreator method) (pyrosetta.rosetta.protocols.cryst.CrystRMS static method) (pyrosetta.rosetta.protocols.cryst.CrystRMSCreator method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMover static method) (pyrosetta.rosetta.protocols.cryst.DockLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMover static method) (pyrosetta.rosetta.protocols.cryst.FitBfactorsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMover static method) (pyrosetta.rosetta.protocols.cryst.LoadDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMover static method) (pyrosetta.rosetta.protocols.cryst.MakeLatticeMoverCreator method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMover static method) (pyrosetta.rosetta.protocols.cryst.MakeLayerMoverCreator method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMover static method) (pyrosetta.rosetta.protocols.cryst.RecomputeDensityMapMoverCreator method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMover static method) (pyrosetta.rosetta.protocols.cryst.ReportGradientsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMover static method) (pyrosetta.rosetta.protocols.cryst.SetCrystWeightMoverCreator method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMover static method) (pyrosetta.rosetta.protocols.cryst.SetRefinementOptionsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMover static method) (pyrosetta.rosetta.protocols.cryst.TagPoseWithRefinementStatsMoverCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfo static method) (pyrosetta.rosetta.protocols.cryst.UpdateCrystInfoCreator method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMover static method) (pyrosetta.rosetta.protocols.cryst.UpdateSolventMoverCreator method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomain static method) (pyrosetta.rosetta.protocols.cutoutdomain.CutOutDomainCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrankshaftFlipMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateAngleConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateDistanceConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraint static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CreateTorsionConstraintCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepRigidBodyPermutationMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilter static method) (pyrosetta.rosetta.protocols.cyclic_peptide.CycpepSymmetryFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.FlipChiralityMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilter static method) (pyrosetta.rosetta.protocols.cyclic_peptide.OversaturatedHbondAcceptorFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideCyclizeMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilter static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsFilterCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetric static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideInternalHbondsMetricCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMover static method) (pyrosetta.rosetta.protocols.cyclic_peptide.PeptideStubMoverCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelector static method) (pyrosetta.rosetta.protocols.cyclic_peptide.RamaMutationSelectorCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlign static method) (pyrosetta.rosetta.protocols.cyclic_peptide.SymmetricCycpepAlignCreator method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutations static method) (pyrosetta.rosetta.protocols.cyclic_peptide.TryDisulfPermutationsCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.BetaSheetArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.BlueprintArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.CompoundArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.DeNovoArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.MotifArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.PoseArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect static method) (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitectCreator method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing static method) (pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing static method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGenerator static method) (pyrosetta.rosetta.protocols.denovo_design.constraints.FileConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover static method) (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilter static method) (pyrosetta.rosetta.protocols.denovo_design.filters.CavityVolumeFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilter static method) (pyrosetta.rosetta.protocols.denovo_design.filters.ExposedHydrophobicsFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilter static method) (pyrosetta.rosetta.protocols.denovo_design.filters.PreProlineFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilter static method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSPredictionFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilter static method) (pyrosetta.rosetta.protocols.denovo_design.filters.SSShapeComplementarityFilterCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.AddSegmentDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.AlignResiduesMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.BridgeChainsMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.DeclareStructureDataCovalentBondMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.ExtendChainMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesign static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FastDesignCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldTreeFromFoldGraphMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.MakeAsymmetricStructureDataMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.RotateSegmentMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.SealFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.SetResidueAliasMoverCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelector static method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.NamedSegmentSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelector static method) (pyrosetta.rosetta.protocols.denovo_design.residue_selectors.PairedSheetResidueSelectorCreator method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation static method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperationCreator method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover static method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMoverCreator method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNA static method) (pyrosetta.rosetta.protocols.dna.DesignProteinBackboneAroundDNACreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMover static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMinMoverCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesign static method) (pyrosetta.rosetta.protocols.dna.DnaInterfaceMultiStateDesignCreator method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePacker static method) (pyrosetta.rosetta.protocols.dna.DnaInterfacePackerCreator method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface static method) (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterfaceCreator method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDna static method) (pyrosetta.rosetta.protocols.dna.SeparateDnaFromNonDnaCreator method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplings static method) (pyrosetta.rosetta.protocols.dna.WatsonCrickRotamerCouplingsCreator method) (pyrosetta.rosetta.protocols.dna_dock.DNAClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.dna_dock.PropagateClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMover static method) (pyrosetta.rosetta.protocols.docking.ConformerSwitchMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacy static method) (pyrosetta.rosetta.protocols.docking.DockingHighResLegacyCreator method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbation static method) (pyrosetta.rosetta.protocols.docking.DockingInitialPerturbationCreator method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingPrepackProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingProtocol static method) (pyrosetta.rosetta.protocols.docking.DockingProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContact static method) (pyrosetta.rosetta.protocols.docking.DockingSlideIntoContactCreator method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocol static method) (pyrosetta.rosetta.protocols.docking.DockMCMProtocolCreator method) (pyrosetta.rosetta.protocols.docking.DockMinMover static method) (pyrosetta.rosetta.protocols.docking.DockMinMoverCreator method) (pyrosetta.rosetta.protocols.docking.DockSetupMover static method) (pyrosetta.rosetta.protocols.docking.DockSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMover static method) (pyrosetta.rosetta.protocols.docking.EnsureExclusivelySharedJumpMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMover static method) (pyrosetta.rosetta.protocols.docking.membrane.MPDockingSetupMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.MPFindInterfaceMoverCreator method) (pyrosetta.rosetta.protocols.docking.membrane.QuickRelaxPartnersSeparatelyCreator method) (pyrosetta.rosetta.protocols.docking.stateless.SaneDockingProtocol static method) (pyrosetta.rosetta.protocols.docking.TemperedDockingCreator method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMover static method) (pyrosetta.rosetta.protocols.drug_design.ApplyChemistryMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMover static method) (pyrosetta.rosetta.protocols.drug_design.bcl.BCLFragmentMutateMoverCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetric static method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricCreator method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMover static method) (pyrosetta.rosetta.protocols.drug_design.RDKitMetricsMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMover static method) (pyrosetta.rosetta.protocols.electron_density.BfactorFittingMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.DensityZscores static method) (pyrosetta.rosetta.protocols.electron_density.DensityZscoresCreator method) (pyrosetta.rosetta.protocols.electron_density.ReportFSC static method) (pyrosetta.rosetta.protocols.electron_density.ReportFSCCreator method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensities static method) (pyrosetta.rosetta.protocols.electron_density.ScaleMapIntensitiesCreator method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover static method) (pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMoverCreator method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMover static method) (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingRefinementMoverCreator method) (pyrosetta.rosetta.protocols.environment.claims.CutBiasClaim static method) (pyrosetta.rosetta.protocols.environment.claims.JumpClaim static method) (pyrosetta.rosetta.protocols.environment.claims.TorsionClaim static method) (pyrosetta.rosetta.protocols.environment.claims.VirtResClaim static method) (pyrosetta.rosetta.protocols.environment.claims.XYZClaim static method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCM static method) (pyrosetta.rosetta.protocols.environment.CoMTrackerCMCreator method) (pyrosetta.rosetta.protocols.environment.EnvMover static method) (pyrosetta.rosetta.protocols.environment.EnvMoverCreator method) (pyrosetta.rosetta.protocols.environment.ScriptCM static method) (pyrosetta.rosetta.protocols.environment.ScriptCMCreator method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers static method) (pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts static method) (pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs static method) (pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator method) (pyrosetta.rosetta.protocols.enzdes.BackboneSampler static method) (pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface static method) (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter static method) (pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter static method) (pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize static method) (pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter static method) (pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilter static method) (pyrosetta.rosetta.protocols.enzdes.LigBurialFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilter static method) (pyrosetta.rosetta.protocols.enzdes.LigDSasaFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilter static method) (pyrosetta.rosetta.protocols.enzdes.LigInterfaceEnergyFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedy static method) (pyrosetta.rosetta.protocols.enzdes.PackRotamersMoverPartGreedyCreator method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover static method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMoverCreator method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighter static method) (pyrosetta.rosetta.protocols.enzdes.ProteinLigandInterfaceUpweighterOperationCreator method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilter static method) (pyrosetta.rosetta.protocols.enzdes.RemoveLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilter static method) (pyrosetta.rosetta.protocols.enzdes.RepackWithoutLigandFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilter static method) (pyrosetta.rosetta.protocols.enzdes.ResidueConformerFilterCreator method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehavior static method) (pyrosetta.rosetta.protocols.enzdes.SetCatalyticResPackBehaviorCreator method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMover static method) (pyrosetta.rosetta.protocols.enzdes.UpdateEnzdesHeaderMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.DNAMethyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.GlycosyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.KinaseMoverCreator method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMover static method) (pyrosetta.rosetta.protocols.enzymatic_movers.NTerminalAcetyltransferaseMoverCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.esm_perplexity.PerResidueEsmProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric static method) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetricCreator method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost static method) (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCostFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinder static method) (pyrosetta.rosetta.protocols.evolution.AlignmentAAFinderFilterCreator method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter static method) (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserterFilterCreator method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover static method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMoverCreator method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutation static method) (pyrosetta.rosetta.protocols.evolution.NucleotideMutationCreator method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMover static method) (pyrosetta.rosetta.protocols.farnesyl.InstallFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMover static method) (pyrosetta.rosetta.protocols.farnesyl.SampleFarnesylMoverCreator method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures static method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures static method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures static method) (pyrosetta.rosetta.protocols.features.AtomTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeatures static method) (pyrosetta.rosetta.protocols.features.BetaTurnDetectionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeatures static method) (pyrosetta.rosetta.protocols.features.ChargeChargeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.DdGFeatures static method) (pyrosetta.rosetta.protocols.features.DdGFeaturesCreator method) (pyrosetta.rosetta.protocols.features.FeaturesReporterCreator method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeatures static method) (pyrosetta.rosetta.protocols.features.GeometricSolvationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondFeatures static method) (pyrosetta.rosetta.protocols.features.HBondFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HBondParameterFeatures static method) (pyrosetta.rosetta.protocols.features.HBondParameterFeaturesCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTest static method) (pyrosetta.rosetta.protocols.features.helixAssembly.ConcurrencyTestCreator method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeatures static method) (pyrosetta.rosetta.protocols.features.helixAssembly.HelixBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.HelixCapFeatures static method) (pyrosetta.rosetta.protocols.features.HelixCapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMover static method) (pyrosetta.rosetta.protocols.features.InterfaceDdGMoverCreator method) (pyrosetta.rosetta.protocols.features.InterfaceFeatures static method) (pyrosetta.rosetta.protocols.features.InterfaceFeaturesCreator method) (pyrosetta.rosetta.protocols.features.JobDataFeatures static method) (pyrosetta.rosetta.protocols.features.JobDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeatures static method) (pyrosetta.rosetta.protocols.features.LoopAnchorFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ModelFeatures static method) (pyrosetta.rosetta.protocols.features.ModelFeaturesCreator method) (pyrosetta.rosetta.protocols.features.OrbitalsFeatures static method) (pyrosetta.rosetta.protocols.features.OrbitalsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PairFeatures static method) (pyrosetta.rosetta.protocols.features.PairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PdbDataFeatures static method) (pyrosetta.rosetta.protocols.features.PdbDataFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeatures static method) (pyrosetta.rosetta.protocols.features.PoseCommentsFeaturesCreator method) (pyrosetta.rosetta.protocols.features.PoseConformationFeatures static method) (pyrosetta.rosetta.protocols.features.PoseConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinBackboneAtomAtomPairFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinBackboneTorsionAngleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinBondGeometryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinRMSDFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeatures static method) (pyrosetta.rosetta.protocols.features.ProteinRMSDNoSuperpositionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures static method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ReportToDB static method) (pyrosetta.rosetta.protocols.features.ReportToDBCreator method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueBurialFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueConformationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueGridScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueSecondaryStructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueTotalScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeatures static method) (pyrosetta.rosetta.protocols.features.ResidueTypesFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeatures static method) (pyrosetta.rosetta.protocols.features.RotamerBoltzmannWeightFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerFeatures static method) (pyrosetta.rosetta.protocols.features.RotamerFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeatures static method) (pyrosetta.rosetta.protocols.features.RotamerRecoveryFeaturesCreator method) (pyrosetta.rosetta.protocols.features.RuntimeFeatures static method) (pyrosetta.rosetta.protocols.features.RuntimeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeatures static method) (pyrosetta.rosetta.protocols.features.SaltBridgeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeatures static method) (pyrosetta.rosetta.protocols.features.ScoreFunctionFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeatures static method) (pyrosetta.rosetta.protocols.features.ScoreTypeFeaturesCreator method) (pyrosetta.rosetta.protocols.features.ScreeningFeatures static method) (pyrosetta.rosetta.protocols.features.ScreeningFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeatures static method) (pyrosetta.rosetta.protocols.features.SecondaryStructureSegmentFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeatures static method) (pyrosetta.rosetta.protocols.features.SimpleMetricFeaturesCreator method) (pyrosetta.rosetta.protocols.features.SmotifFeatures static method) (pyrosetta.rosetta.protocols.features.SmotifFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeatures static method) (pyrosetta.rosetta.protocols.features.strand_assembly.SandwichFeaturesCreator method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures static method) (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureFeatures static method) (pyrosetta.rosetta.protocols.features.StructureFeaturesCreator method) (pyrosetta.rosetta.protocols.features.StructureScoresFeatures static method) (pyrosetta.rosetta.protocols.features.StructureScoresFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TaskOperationFeatures static method) (pyrosetta.rosetta.protocols.features.TaskOperationFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TotalScoreFeatures static method) (pyrosetta.rosetta.protocols.features.TotalScoreFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeatures static method) (pyrosetta.rosetta.protocols.features.TrajectoryMapFeaturesCreator method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDB static method) (pyrosetta.rosetta.protocols.features.TrajectoryReportToDBCreator method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeatures static method) (pyrosetta.rosetta.protocols.features.UnrecognizedAtomFeaturesCreator method) (pyrosetta.rosetta.protocols.features.WaterFeatures static method) (pyrosetta.rosetta.protocols.features.WaterFeaturesCreator method) (pyrosetta.rosetta.protocols.filters.CalculatorFilter static method) (pyrosetta.rosetta.protocols.filters.CalculatorFilterCreator method) (pyrosetta.rosetta.protocols.filters.CombinedFilter static method) (pyrosetta.rosetta.protocols.filters.CombinedFilterCreator method) (pyrosetta.rosetta.protocols.filters.CompoundFilter static method) (pyrosetta.rosetta.protocols.filters.CompoundFilterCreator method) (pyrosetta.rosetta.protocols.filters.ContingentFilter static method) (pyrosetta.rosetta.protocols.filters.ContingentFilterCreator method) (pyrosetta.rosetta.protocols.filters.FalseFilter static method) (pyrosetta.rosetta.protocols.filters.FalseFilterCreator method) (pyrosetta.rosetta.protocols.filters.FilterCreator method) (pyrosetta.rosetta.protocols.filters.FilterFactory method) (pyrosetta.rosetta.protocols.filters.FilterValueMetric static method) (pyrosetta.rosetta.protocols.filters.FilterValueMetricCreator method) (pyrosetta.rosetta.protocols.filters.IfThenFilter static method) (pyrosetta.rosetta.protocols.filters.IfThenFilterCreator method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilter static method) (pyrosetta.rosetta.protocols.filters.MoveBeforeFilterCreator method) (pyrosetta.rosetta.protocols.filters.ReplicateFilter static method) (pyrosetta.rosetta.protocols.filters.ReplicateFilterCreator method) (pyrosetta.rosetta.protocols.filters.StochasticFilter static method) (pyrosetta.rosetta.protocols.filters.StochasticFilterCreator method) (pyrosetta.rosetta.protocols.filters.TimeFilter static method) (pyrosetta.rosetta.protocols.filters.TimeFilterCreator method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilter static method) (pyrosetta.rosetta.protocols.filters.TrueFalseFilterCreator method) (pyrosetta.rosetta.protocols.filters.TrueFilter static method) (pyrosetta.rosetta.protocols.filters.TrueFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDR static method) (pyrosetta.rosetta.protocols.fldsgn.BluePrintBDRCreator method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutation static method) (pyrosetta.rosetta.protocols.fldsgn.CircularPermutationCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixBendFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixKinkFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.HelixPairingFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.NcontactsFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureCountFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureHasResidueFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels static method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevelsCreator method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter static method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilterCreator method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMover static method) (pyrosetta.rosetta.protocols.fldsgn.MatchResiduesMoverCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotential static method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetAACompositionPotentialCreator method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies static method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergiesCreator method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGenerator static method) (pyrosetta.rosetta.protocols.fldsgn.SheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator static method) (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocol static method) (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingProtocolCreator method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesign static method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator method) (pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack static method) (pyrosetta.rosetta.protocols.flxbb.InterlockAroma static method) (pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation static method) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGenerator static method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.AutomaticSheetConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGenerator static method) (pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator.SegmentedAtomPairConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilter static method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ConstraintFulfilmentFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilter static method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.RmsdFromResidueSelectorFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilter static method) (pyrosetta.rosetta.protocols.fold_from_loops.filters.ScorePoseSegmentFromResidueSelectorFilterCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.AlignByResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.DisplayPoseLabelsMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.MoveMapFactoryToNamedMoveMapMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ReleaseConstraintFromResidueMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.ResidueLabelsToPymolSelectionMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SavePDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.SplitAndMixPoseMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover static method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMoverCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelector static method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ConstraintResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelector static method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.CutpointResidueSelectorCreator method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelector static method) (pyrosetta.rosetta.protocols.fold_from_loops.selectors.ProteinResidueSelectorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG static method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGenerator static method) (pyrosetta.rosetta.protocols.forge.constraints.NtoCConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCsts static method) (pyrosetta.rosetta.protocols.forge.constraints.RemoveRemodelCstsCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMoverCreator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinks static method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelRotamerLinksCreator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityCstGeneratorCreator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG static method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilter static method) (pyrosetta.rosetta.protocols.frag_picker.FragmentScoreFilterCreator method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKIC static method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.GeneralizedKICCreator method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocol static method) (pyrosetta.rosetta.protocols.glycan_docking.GlycanDockProtocolCreator method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocol static method) (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingProtocolCreator method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover static method) (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover static method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.DeleteRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.InsertPoseIntoPoseMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.KeepRegionMoverCreator method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMover static method) (pyrosetta.rosetta.protocols.grafting.simple_movers.ReplaceRegionMoverCreator method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork static method) (pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetworkCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNet static method) (pyrosetta.rosetta.protocols.hbnet.HBNetCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetScore static method) (pyrosetta.rosetta.protocols.hbnet.HBNetScoreFilterCreator method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface static method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterfaceCreator method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelector static method) (pyrosetta.rosetta.protocols.hbnet.UnsatSelectorCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler static method) (pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler static method) (pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter static method) (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundle static method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle static method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix static method) (pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbe static method) (pyrosetta.rosetta.protocols.hotspot_hashing.movers.PlaceSurfaceProbeCreator method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbation static method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionPerturbationCreator method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSampler static method) (pyrosetta.rosetta.protocols.hybridization.BackboneTorsionSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.CartesianSampler static method) (pyrosetta.rosetta.protocols.hybridization.CartesianSamplerCreator method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocol static method) (pyrosetta.rosetta.protocols.hybridization.HybridizeProtocolCreator method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover static method) (pyrosetta.rosetta.protocols.idealize.IdealizeMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter static method) (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilterCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover static method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMoverCreator method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMover static method) (pyrosetta.rosetta.protocols.indexed_structure_store.movers.SegmentSequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputter static method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.PDBChunkLibraryInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputter static method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputter static method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputter static method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PDBPoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputter static method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.SilentFilePoseInputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputterCreator method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter static method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputterCreator method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMover static method) (pyrosetta.rosetta.protocols.kinematic_closure.BalancedKicMoverCreator method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMover static method) (pyrosetta.rosetta.protocols.kinematic_closure.KicMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragments static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAddStartnodeFragmentsCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyEnumerateAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGivenPathAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyGreedyAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyMonteCarloAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFile static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFile static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyReadRepeatNativeRotamersFileCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMover static method) (pyrosetta.rosetta.protocols.legacy_sewing.LegacyRepeatAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirement static method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalLengthRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyGlobalRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyIntraSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirement static method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyResidueRetentionRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirement static method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentDsspRequirementCreator method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirement static method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacySegmentLengthRequirementCreator method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens static method) (pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate static method) (pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF static method) (pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer static method) (pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock static method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigand static method) (pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDocker static method) (pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder static method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader static method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator static method) (pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandArea static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesign static method) (pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone static method) (pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter static method) (pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder static method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader static method) (pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformers static method) (pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryHbondFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFBinaryOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFChargeFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFElecFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFEtableFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondCreator method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFHbondFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunction static method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFOrbitalFunctionCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Rotate static method) (pyrosetta.rosetta.protocols.ligand_docking.RotateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Rotates static method) (pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogether static method) (pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator method) (pyrosetta.rosetta.protocols.ligand_docking.StartFrom static method) (pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Transform static method) (pyrosetta.rosetta.protocols.ligand_docking.TransformCreator method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble static method) (pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator method) (pyrosetta.rosetta.protocols.ligand_docking.Translate static method) (pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile static method) (pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapper static method) (pyrosetta.rosetta.protocols.loop_build.LoopmodelWrapperCreator method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow static method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindowCreator method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtension static method) (pyrosetta.rosetta.protocols.loop_grower.FragmentExtensionCreator method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler static method) (pyrosetta.rosetta.protocols.loop_modeler.LoopModelerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol static method) (pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.MinimizationRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RepackingRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefiner static method) (pyrosetta.rosetta.protocols.loop_modeling.refiners.RotamerTrialsRefinerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSampler static method) (pyrosetta.rosetta.protocols.loop_modeling.samplers.LegacyKicSamplerCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroid static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForCentroidCreator method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatom static method) (pyrosetta.rosetta.protocols.loop_modeling.utilities.PrepareForFullatomCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifier static method) (pyrosetta.rosetta.protocols.loophash.LoopHashDiversifierCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoader static method) (pyrosetta.rosetta.protocols.loophash.LoopHashLibraryLoaderCreator method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper static method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapperCreator method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilter static method) (pyrosetta.rosetta.protocols.loops.filters.LoopAnalyzerFilterCreator method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoops static method) (pyrosetta.rosetta.protocols.loops.FoldTreeFromLoopsCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMover static method) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.CCDLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMover static method) (pyrosetta.rosetta.protocols.loops.loop_closure.jacobi.JacobiLoopClosureMoverCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCM static method) (pyrosetta.rosetta.protocols.loops.loop_mover.LoopCMCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KIC static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_Moves static method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD_MovesCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_Backrub static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_BackrubCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCDCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KIC static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_KICCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainer static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopRefineInnerCycleContainerCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrial static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.RepackTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrial static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.ShearMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrial static method) (pyrosetta.rosetta.protocols.loops.loop_mover.refine.SmallMinCCDTrialCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefiner static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDatabaseDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoader static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerLoaderCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefiner static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsExplicitDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefiner static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsFileDefinerCreator method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefiner static method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsStringDefinerCreator method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoader static method) (pyrosetta.rosetta.protocols.loops.LoopsFileLoaderCreator method) (pyrosetta.rosetta.protocols.match.MatcherMover static method) (pyrosetta.rosetta.protocols.match.MatcherMoverCreator method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation static method) (pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilter static method) (pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover static method) (pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues static method) (pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter static method) (pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover static method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter static method) (pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover static method) (pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SymDofMover static method) (pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter static method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.md.CartesianMD static method) (pyrosetta.rosetta.protocols.md.CartesianMDCreator method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover static method) (pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraint static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraint static method) (pyrosetta.rosetta.protocols.membrane.AddMembraneSpanTermZConstraintCreator method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMover static method) (pyrosetta.rosetta.protocols.membrane.AddMPLigandMoverCreator method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder static method) (pyrosetta.rosetta.protocols.membrane.AqueousPoreFinderCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelix static method) (pyrosetta.rosetta.protocols.membrane.benchmark.MakeCanonicalHelixCreator method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAngles static method) (pyrosetta.rosetta.protocols.membrane.benchmark.SampleTiltAnglesCreator method) (pyrosetta.rosetta.protocols.membrane.FlipMover static method) (pyrosetta.rosetta.protocols.membrane.FlipMoverCreator method) (pyrosetta.rosetta.protocols.membrane.HelixFromSequenceCreator method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMover static method) (pyrosetta.rosetta.protocols.membrane.MembranePositionFromTopologyMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibility static method) (pyrosetta.rosetta.protocols.membrane.MPLipidAccessibilityCreator method) (pyrosetta.rosetta.protocols.membrane.MPMutateRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.MPQuickRelaxMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMover static method) (pyrosetta.rosetta.protocols.membrane.OptimizeMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.OptimizeProteinEmbeddingMover static 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 static method) (pyrosetta.rosetta.protocols.membrane.SetMembranePositionMoverCreator method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMover static method) (pyrosetta.rosetta.protocols.membrane.SpinAroundPartnerMoverCreator method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.symmetry.SymmetricAddMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TiltMover static method) (pyrosetta.rosetta.protocols.membrane.TiltMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.TransformIntoMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.TranslationRotationMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMover static method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeEmbeddingMoverCreator method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMover static method) (pyrosetta.rosetta.protocols.membrane.visualize.VisualizeMembraneMoverCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSampler static method) (pyrosetta.rosetta.protocols.membrane_benchmark.MembraneEnergyLandscapeSamplerCreator method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMover static method) (pyrosetta.rosetta.protocols.membrane_benchmark.PeptideOrientationMoverCreator method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMover static method) (pyrosetta.rosetta.protocols.metal_interface.RemoveMetalConnectionsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMover static method) (pyrosetta.rosetta.protocols.minimization_packing.BoltzmannRotamerMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMover static method) (pyrosetta.rosetta.protocols.minimization_packing.DisulfideOptimizationMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.EnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.MinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.MinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMover static method) (pyrosetta.rosetta.protocols.minimization_packing.MinPackMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazy static method) (pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMoverLazyCreator method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.PertMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RepackSidechainsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.RotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.SaneMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.SetReturningPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymEnergyCutRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymPackRotamersMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.SymRotamerTrialsMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.symmetry.TaskAwareSymMinMoverCreator method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMover static method) (pyrosetta.rosetta.protocols.minimization_packing.TaskAwareMinMoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer static method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealerCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecover static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloRecoverCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloReset static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloResetCreator method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTest static method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloTestCreator method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover static method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMoverCreator method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftCreator method) (pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover static method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPacker static method) (pyrosetta.rosetta.protocols.motifs.MotifDnaPackerCreator method) (pyrosetta.rosetta.protocols.moves.DsspMover static method) (pyrosetta.rosetta.protocols.moves.DsspMoverCreator method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMover static method) (pyrosetta.rosetta.protocols.moves.FilterReportAsPoseExtraScoresMoverCreator method) (pyrosetta.rosetta.protocols.moves.IfMover static method) (pyrosetta.rosetta.protocols.moves.IfMoverCreator method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover static method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverCreator method) (pyrosetta.rosetta.protocols.moves.MoverFactory method) (pyrosetta.rosetta.protocols.moves.PyMOLMover static method) (pyrosetta.rosetta.protocols.moves.PyMOLMoverCreator method) (pyrosetta.rosetta.protocols.moves.RampingMover static method) (pyrosetta.rosetta.protocols.moves.RampingMoverCreator method) (pyrosetta.rosetta.protocols.moves.RandomMover static method) (pyrosetta.rosetta.protocols.moves.RandomMoverCreator method) (pyrosetta.rosetta.protocols.moves.SequenceMover static method) (pyrosetta.rosetta.protocols.moves.SequenceMoverCreator method) (pyrosetta.rosetta.protocols.moves.SwitchMover static method) (pyrosetta.rosetta.protocols.moves.SwitchMoverCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetric static method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.JumpMetricCreator method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetric static method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics.SequenceMetricCreator method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocol static method) (pyrosetta.rosetta.protocols.ncbb.NcbbDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMover static method) (pyrosetta.rosetta.protocols.ncbb.oop.OopCreatorMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocol static method) (pyrosetta.rosetta.protocols.ncbb.oop.OopDockDesignProtocolCreator method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMover static method) (pyrosetta.rosetta.protocols.ncbb.ResidueReplacementRebuildMoverCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructFinderCreator method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMover static method) (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMoverCreator method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMover static method) (pyrosetta.rosetta.protocols.nmr.ParaNMRScoreMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover static method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator method) (pyrosetta.rosetta.protocols.nmr.pre.PREMover static method) (pyrosetta.rosetta.protocols.nmr.pre.PREMoverCreator method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizer static method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMinimizerCreator method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMover static method) (pyrosetta.rosetta.protocols.normalmode.NormalModeRelaxMoverCreator method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighter static method) (pyrosetta.rosetta.protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperationCreator method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoader static method) (pyrosetta.rosetta.protocols.parser.ConstraintGeneratorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoader static method) (pyrosetta.rosetta.protocols.parser.DatabaseSessionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.DataLoaderCreator method) (pyrosetta.rosetta.protocols.parser.FragmentReader static method) (pyrosetta.rosetta.protocols.parser.FragSetLoader static method) (pyrosetta.rosetta.protocols.parser.FragSetLoaderCreator method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoader static method) (pyrosetta.rosetta.protocols.parser.JumpSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoader static method) (pyrosetta.rosetta.protocols.parser.MonteCarloLoaderCreator method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoader static method) (pyrosetta.rosetta.protocols.parser.MoveMapFactoryLoaderCreator method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoader static method) (pyrosetta.rosetta.protocols.parser.PackerPaletteLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoader static method) (pyrosetta.rosetta.protocols.parser.ResidueSelectorLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoader static method) (pyrosetta.rosetta.protocols.parser.ResLvlTaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoader static method) (pyrosetta.rosetta.protocols.parser.ScoreFunctionLoaderCreator method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoader static method) (pyrosetta.rosetta.protocols.parser.SimpleMetricLoaderCreator method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoader static method) (pyrosetta.rosetta.protocols.parser.TaskOperationLoaderCreator method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotential static method) (pyrosetta.rosetta.protocols.pb_potential.SetupPoissonBoltzmannPotentialCreator method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequences static method) (pyrosetta.rosetta.protocols.pdbinfo_manipulations.AlignPDBInfoToSequencesCreator method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter static method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilterCreator method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMover static method) (pyrosetta.rosetta.protocols.pose_creation.ExtendedPoseMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMover static method) (pyrosetta.rosetta.protocols.pose_creation.MakeJunctionsMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMover static method) (pyrosetta.rosetta.protocols.pose_creation.MakePolyXMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMover static method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBatOverlapMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMover static method) (pyrosetta.rosetta.protocols.pose_creation.MergePDBMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMover static method) (pyrosetta.rosetta.protocols.pose_creation.PoseFromSequenceMoverCreator method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover static method) (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModeling static method) (pyrosetta.rosetta.protocols.pose_length_moves.AnalyzeLoopModelingCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.ConnectChainsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.FixAllLoopsMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMover static method) (pyrosetta.rosetta.protocols.pose_length_moves.InsertResMoverCreator method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloser static method) (pyrosetta.rosetta.protocols.pose_length_moves.NearNativeLoopCloserCreator method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporter static method) (pyrosetta.rosetta.protocols.pose_reporters.EnergyReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporter static method) (pyrosetta.rosetta.protocols.pose_reporters.FilterReporterCreator method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporter static method) (pyrosetta.rosetta.protocols.pose_reporters.RMSDReporterCreator method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelector static method) (pyrosetta.rosetta.protocols.pose_selectors.AndSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelector static method) (pyrosetta.rosetta.protocols.pose_selectors.ClusterPoseSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.Filter static method) (pyrosetta.rosetta.protocols.pose_selectors.FilterCreator method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelector static method) (pyrosetta.rosetta.protocols.pose_selectors.OrSelectorCreator method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByProperty static method) (pyrosetta.rosetta.protocols.pose_selectors.TopNByPropertyCreator method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorer static method) (pyrosetta.rosetta.protocols.pose_sewing.filters.CoreScorerCreator method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilter static method) (pyrosetta.rosetta.protocols.pose_sewing.filters.HasDisulfideFilterCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.AddFlankingVirtualResiduesMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.BlockwiseAnalysisMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.OmnibusDisulfideAnalysisLabelerMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.PickRandomSegmentMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover static method) (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMoverCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwisePoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.BlockwiseShapeCompMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.MinimumInterAlphaDistanceMetricCreator method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetric static method) (pyrosetta.rosetta.protocols.pose_sewing.simple_metrics.WindowPoseCompMotifMetricCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AtomicContactCountFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.AverageDegreeFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BindingStrainFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.ClashWithTargetFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DesignableResiduesFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FNatFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.InterfaceHolesFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.IRmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.LRmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.RmsdSimpleFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SequenceRecoveryFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SpecificResiduesNearInterfaceFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.SSamountFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilter static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.StubScoreLoopsFilterCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.Torsion static method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.TorsionCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreakCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspots static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddSidechainConstraintsToHotspotsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BackrubDDMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BestHotspotCstMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPose static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.BuildAlaPoseCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbonds static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DesignMinimizeHbondsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DisulfideMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechains static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.DockWithHotspotMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycle static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycle static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.FavorNonNativeResiduePreCycleCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotDisjointedFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.HotspotHasherMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.InterfaceRecapitulationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinder static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopFinderCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChange static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopLengthChangeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLine static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopMoverFromCommandLineCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOver static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopOverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodel static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.LoopRemodelCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspot static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.MapHotspotCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransform static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PatchdockTransformCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PeptideStapleDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementAuctionMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlacementMinimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoop static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceOnLoopCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceStubMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.PrepackMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ProteinInterfaceMultiStateDesignMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutation static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RandomMutationCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimize static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.RepackMinimizeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechains static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SaveAndRetrieveSidechainsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTreeCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactorCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsLoopsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetupHotspotConstraintsMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.ShoveResidueMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SpinMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SubroutineMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCsts static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TaskAwareCstsCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMover static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TopologyBrokerMoverCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamers static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.TryRotamersCreator method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLB static method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBCreator method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMover static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNMoverCreator method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetric static method) (pyrosetta.rosetta.protocols.protein_mpnn.ProteinMPNNProbabilitiesMetricCreator method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric static method) (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetricCreator method) (pyrosetta.rosetta.protocols.qsar.qsarCreator method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage static method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemageCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.AtrGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ChargeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ClassicGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScore static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LigandPropertyScoreCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSMultiGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.PCSSingleGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.RepGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoader static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ScoringGridLoaderCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.ShapeGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SiteGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.SolvationMetaGridCreator method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGrid static method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.VdwGridCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader static method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoaderCreator method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric static method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetricCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.ConfChangeMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.IdealizeHelicesMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.MakeStarTopologyMoverCreator method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMover static method) (pyrosetta.rosetta.protocols.rbsegment_relax.OptimizeThreadingMoverCreator method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizer static method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalMinimizerCreator method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover static method) (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMoverCreator method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequence static method) (pyrosetta.rosetta.protocols.recon_design.FindConsensusSequenceCreator method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilter static method) (pyrosetta.rosetta.protocols.recon_design.FitnessFilterCreator method) (pyrosetta.rosetta.protocols.recon_design.MSDMover static method) (pyrosetta.rosetta.protocols.recon_design.MSDMoverCreator method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMover static method) (pyrosetta.rosetta.protocols.relax.AcceptToBestMoverCreator method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover static method) (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMoverCreator method) (pyrosetta.rosetta.protocols.relax.ClassicRelaxCreator method) (pyrosetta.rosetta.protocols.relax.FastRelax static method) (pyrosetta.rosetta.protocols.relax.FastRelaxCreator method) (pyrosetta.rosetta.protocols.relax.LocalRelax static method) (pyrosetta.rosetta.protocols.relax.LocalRelaxCreator method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover static method) (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMoverCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMover static method) (pyrosetta.rosetta.protocols.relax.membrane.MPFastRelaxMoverCreator method) (pyrosetta.rosetta.protocols.relax.membrane.MPRangeRelaxMover static method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelax static method) (pyrosetta.rosetta.protocols.relax.RepeatProteinRelaxCreator method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelector static method) (pyrosetta.rosetta.protocols.residue_selectors.HBondSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelector static method) (pyrosetta.rosetta.protocols.residue_selectors.LigandMetalContactSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelector static method) (pyrosetta.rosetta.protocols.residue_selectors.NativeSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelector static method) (pyrosetta.rosetta.protocols.residue_selectors.StoredResidueSubsetSelectorCreator method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMover static method) (pyrosetta.rosetta.protocols.residue_selectors.StoreResidueSubsetMoverCreator method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelector static method) (pyrosetta.rosetta.protocols.residue_selectors.TaskSelectorCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbNoCenterMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTiltMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover static method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMoverCreator method) (pyrosetta.rosetta.protocols.rigid.RollMover static method) (pyrosetta.rosetta.protocols.rigid.RollMoverCreator method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCM static method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyCMCreator method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMover static method) (pyrosetta.rosetta.protocols.rigid.UniformRigidBodyMoverCreator method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMover static method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoProtocolMoverCreator method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocol static method) (pyrosetta.rosetta.protocols.rna.denovo.RNA_DeNovoProtocolCreator method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2Protocol static method) (pyrosetta.rosetta.protocols.rna.movers.ERRASER2ProtocolCreator method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover static method) (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Coarsify static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_CoarsifyCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNA_Decoarsify static method) (pyrosetta.rosetta.protocols.rna.movers.RNA_DecoarsifyCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMover static method) (pyrosetta.rosetta.protocols.rna.movers.RNAIdealizeMoverCreator method) (pyrosetta.rosetta.protocols.rna.movers.RNAThreadAndMinimizeMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.AdditionalOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapper static method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultipleOutputWrapperCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover static method) (pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMoverCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol static method) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocolCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorCreator method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMover static method) (pyrosetta.rosetta.protocols.rosetta_scripts.SavePoseMoverCreator method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMover static method) (pyrosetta.rosetta.protocols.rotamer_recovery.RotamerRecoveryMoverCreator method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilter static method) (pyrosetta.rosetta.protocols.score_filters.GeometryFilterCreator method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilter static method) (pyrosetta.rosetta.protocols.score_filters.ScoreCutoffFilterCreator method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilter static method) (pyrosetta.rosetta.protocols.score_filters.ScoreTypeFilterCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGenerator static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CAcstGeneratorCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFold static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CloseFoldCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCst static method) (pyrosetta.rosetta.protocols.seeded_abinitio.CoordinateCstCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoops static method) (pyrosetta.rosetta.protocols.seeded_abinitio.DefineMovableLoopsCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptides static method) (pyrosetta.rosetta.protocols.seeded_abinitio.GrowPeptidesCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTreeCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMover static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedSetupMoverCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizer static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SegmentHybridizerCreator method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegment static method) (pyrosetta.rosetta.protocols.seeded_abinitio.SwapSegmentCreator method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMover static method) (pyrosetta.rosetta.protocols.sewing.hashing.AlignmentFileGeneratorMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.AssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover static method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMoverCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.ClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.DsspSpecificLengthRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.KeepLigandContactsRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.LengthInResiduesRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.LigandClashRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.NonTerminalStartingSegmentRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirement static method) (pyrosetta.rosetta.protocols.sewing.requirements.SizeInSegmentsRequirementCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.LigandScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorerCreator method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer static method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorerCreator method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScan static method) (pyrosetta.rosetta.protocols.simple_ddg.AlaScanFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.ddG static method) (pyrosetta.rosetta.protocols.simple_ddg.ddGCreator method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter static method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScan static method) (pyrosetta.rosetta.protocols.simple_ddg.DdGScanCreator method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilter static method) (pyrosetta.rosetta.protocols.simple_ddg.InterfaceBindingEnergyDensityFilterCreator method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilter static method) (pyrosetta.rosetta.protocols.simple_ddg.SSElementBisectddGFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVector static method) (pyrosetta.rosetta.protocols.simple_filters.AngleToVectorFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilter static method) (pyrosetta.rosetta.protocols.simple_filters.AtomicContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.AtomicDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilter static method) (pyrosetta.rosetta.protocols.simple_filters.AveragePathLengthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter static method) (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilter static method) (pyrosetta.rosetta.protocols.simple_filters.BuriedUnsatHbondFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreak static method) (pyrosetta.rosetta.protocols.simple_filters.ChainBreakFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ChainCountFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter static method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilter static method) (pyrosetta.rosetta.protocols.simple_filters.DisulfideEntropyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilter static method) (pyrosetta.rosetta.protocols.simple_filters.EnergyPerResidueFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ExpiryFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter static method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter static method) (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter static method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter static method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilter static method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHbondsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilter static method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceHydrophobicResidueContactsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilter static method) (pyrosetta.rosetta.protocols.simple_filters.InterfaceSasaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter static method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter static method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter static method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter static method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilter static method) (pyrosetta.rosetta.protocols.simple_filters.MembAccesResidueLipophilicityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilter static method) (pyrosetta.rosetta.protocols.simple_filters.MotifScoreFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilter static method) (pyrosetta.rosetta.protocols.simple_filters.MPSpanAngleFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilter static method) (pyrosetta.rosetta.protocols.simple_filters.MutationsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NeighborTypeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NetChargeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NMerPSSMEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NMerSVMEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilter static method) (pyrosetta.rosetta.protocols.simple_filters.NonSequentialNeighborsFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter static method) (pyrosetta.rosetta.protocols.simple_filters.PackStatFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseComment static method) (pyrosetta.rosetta.protocols.simple_filters.PoseCommentFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilter static method) (pyrosetta.rosetta.protocols.simple_filters.PoseInfoFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilter static method) (pyrosetta.rosetta.protocols.simple_filters.RangeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ReadPoseExtraScoreFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilter static method) (pyrosetta.rosetta.protocols.simple_filters.RepeatParameterFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueBurialFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueChiralityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueCountFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDepthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueIEFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueLipophilicityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSelectionDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResidueSetChainEnergyFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ResiduesInInterfaceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SaveResfileToDiskFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SecretionPredictionFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistance static method) (pyrosetta.rosetta.protocols.simple_filters.SequenceDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter static method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SidechainRmsdFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SimpleHbondsToAtomFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SimpleMetricFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SpanTopologyMatchPoseFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SSElementLengthFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder static method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinderFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder static method) (pyrosetta.rosetta.protocols.simple_filters.StemFinderFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilter static method) (pyrosetta.rosetta.protocols.simple_filters.SymmetricMotifFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareSASAFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TaskAwareScoreTypeFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TerminusDistanceFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TMsAACompFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TMsSpanMembraneFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilter static method) (pyrosetta.rosetta.protocols.simple_filters.TotalSasaFilterCreator method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilter static method) (pyrosetta.rosetta.protocols.simple_filters.Worst9merFilterCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairData static method) (pyrosetta.rosetta.protocols.simple_moves.AddJobPairDataCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddPDBInfoMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraint static method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueCouplingConstraintCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddResidueLabelMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddSapConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMover static method) (pyrosetta.rosetta.protocols.simple_moves.AddSapMathConstraintMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.AlignChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover static method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMover static method) (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover static method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBins static method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.InitializeByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBins static method) (pyrosetta.rosetta.protocols.simple_moves.bin_transitions.PerturbByBinsCreator method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover static method) (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConcatenatePosesMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover static method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover static method) (pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover static method) (pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMover static method) (pyrosetta.rosetta.protocols.simple_moves.CoupledMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBond static method) (pyrosetta.rosetta.protocols.simple_moves.DeclareBondCreator method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMover method) (pyrosetta.rosetta.protocols.simple_moves.DEEROptimizeCoordsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMover static method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover static method) (pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover static method) (pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdb static method) (pyrosetta.rosetta.protocols.simple_moves.DumpPdbCreator method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers static method) (pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamersCreator method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover static method) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfile static method) (pyrosetta.rosetta.protocols.simple_moves.FavorSequenceProfileCreator method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequence static method) (pyrosetta.rosetta.protocols.simple_moves.FavorSymmetricSequenceCreator method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotif static method) (pyrosetta.rosetta.protocols.simple_moves.FoldTreeFromMotifCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover static method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover static method) (pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopology static method) (pyrosetta.rosetta.protocols.simple_moves.MembraneTopologyCreator method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover static method) (pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidue static method) (pyrosetta.rosetta.protocols.simple_moves.MutateResidueCreator method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMover static method) (pyrosetta.rosetta.protocols.simple_moves.PDBReloadMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMover static method) (pyrosetta.rosetta.protocols.simple_moves.PeriodicBoxMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMover static method) (pyrosetta.rosetta.protocols.simple_moves.PoseFromPoseResourceMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMover static method) (pyrosetta.rosetta.protocols.simple_moves.PSSM2BfactorMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover static method) (pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover static method) (pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMover static method) (pyrosetta.rosetta.protocols.simple_moves.RepeatPropagationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA static method) (pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKACreator method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZ static method) (pyrosetta.rosetta.protocols.simple_moves.ReportXYZCreator method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTree static method) (pyrosetta.rosetta.protocols.simple_moves.ResetFoldTreeCreator method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMover static method) (pyrosetta.rosetta.protocols.simple_moves.ResetFullModelInfoMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMover static method) (pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilities static method) (pyrosetta.rosetta.protocols.simple_moves.SampleSequenceFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMover static method) (pyrosetta.rosetta.protocols.simple_moves.SaveProbabilitiesMetricMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMover static method) (pyrosetta.rosetta.protocols.simple_moves.SaveSequenceToCommentsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMover static method) (pyrosetta.rosetta.protocols.simple_moves.ScoreMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMover static method) (pyrosetta.rosetta.protocols.simple_moves.SequenceProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsion static method) (pyrosetta.rosetta.protocols.simple_moves.SetTorsionCreator method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover static method) (pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShearMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover static method) (pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbChiSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SetChiMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMCMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMover static method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.SidechainMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover static method) (pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMover static method) (pyrosetta.rosetta.protocols.simple_moves.SixDoFGridDockMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover static method) (pyrosetta.rosetta.protocols.simple_moves.SmallMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot static method) (pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshotCreator method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMover static method) (pyrosetta.rosetta.protocols.simple_moves.StructProfileMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover static method) (pyrosetta.rosetta.protocols.simple_moves.SuperimposeMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMover static method) (pyrosetta.rosetta.protocols.simple_moves.SwitchChainOrderMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover static method) (pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.TailsScoreMover static method) (pyrosetta.rosetta.protocols.simple_moves.Tumble static method) (pyrosetta.rosetta.protocols.simple_moves.TumbleCreator method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMover static method) (pyrosetta.rosetta.protocols.simple_moves.VirtualRootMoverCreator method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPose static method) (pyrosetta.rosetta.protocols.simple_moves.WriteFiltersToPoseCreator method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMover static method) (pyrosetta.rosetta.protocols.simple_moves.WriteSSEMoverCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack1 static method) (pyrosetta.rosetta.protocols.simple_task_operations.DockingNoRepack2 static method) (pyrosetta.rosetta.protocols.simple_task_operations.InterfaceTaskOperation static method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterface static method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToInterfaceCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoops static method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighbors static method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsAndNeighborsCreator method) (pyrosetta.rosetta.protocols.simple_task_operations.RestrictToLoopsCreator method) (pyrosetta.rosetta.protocols.splice.AlignEndsMover static method) (pyrosetta.rosetta.protocols.splice.AlignEndsMoverCreator method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperation static method) (pyrosetta.rosetta.protocols.splice.DesignInterfacesOperationCreator method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperation static method) (pyrosetta.rosetta.protocols.splice.FindEndpointsOperationCreator method) (pyrosetta.rosetta.protocols.splice.RBInMover static method) (pyrosetta.rosetta.protocols.splice.RBInMoverCreator method) (pyrosetta.rosetta.protocols.splice.RBOutMover static method) (pyrosetta.rosetta.protocols.splice.RBOutMoverCreator method) (pyrosetta.rosetta.protocols.splice.RotLibOut static method) (pyrosetta.rosetta.protocols.splice.RotLibOutCreator method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB static method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDBCreator method) (pyrosetta.rosetta.protocols.splice.Splice static method) (pyrosetta.rosetta.protocols.splice.SpliceCreator method) (pyrosetta.rosetta.protocols.splice.SpliceIn static method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody static method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInCreator method) (pyrosetta.rosetta.protocols.splice.SpliceInTail static method) (pyrosetta.rosetta.protocols.splice.SpliceInTailCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOut static method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody static method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibodyCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutCreator method) (pyrosetta.rosetta.protocols.splice.SpliceOutTail static method) (pyrosetta.rosetta.protocols.splice.SpliceOutTailCreator method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover static method) (pyrosetta.rosetta.protocols.splice.TailSegmentMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.AddMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.DeleteMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.FromScratchMoverCreator method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMover static method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.ResampleMoverCreator method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMover static method) (pyrosetta.rosetta.protocols.struct_fragment.StructFragmentMoverCreator method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoader static method) (pyrosetta.rosetta.protocols.surface_docking.SurfaceVectorLoaderCreator method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMover static method) (pyrosetta.rosetta.protocols.switches.GraftSwitchMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.membrane.MPSymDockMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover static method) (pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetry static method) (pyrosetta.rosetta.protocols.symmetry.DetectSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMover static method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricPoseMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMover static method) (pyrosetta.rosetta.protocols.symmetry.ExtractAsymmetricUnitMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupForSequenceSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupForSymmetryMoverCreator method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMover static method) (pyrosetta.rosetta.protocols.symmetry.SetupNCSMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperation static method) (pyrosetta.rosetta.protocols.task_operations.AlignedThreadOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.ConservativeDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperation static method) (pyrosetta.rosetta.protocols.task_operations.CrystalContactsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThread static method) (pyrosetta.rosetta.protocols.task_operations.DatabaseThreadCreator method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperation static method) (pyrosetta.rosetta.protocols.task_operations.DesignAroundOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.DsspDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperation static method) (pyrosetta.rosetta.protocols.task_operations.ImportUnboundRotamersOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosion static method) (pyrosetta.rosetta.protocols.task_operations.InteractingRotamerExplosionCreator method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperation static method) (pyrosetta.rosetta.protocols.task_operations.JointSequenceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2Operation static method) (pyrosetta.rosetta.protocols.task_operations.LimitAromaChi2OperationCreator method) (pyrosetta.rosetta.protocols.task_operations.LinkResidues static method) (pyrosetta.rosetta.protocols.task_operations.LinkResiduesCreator method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealer static method) (pyrosetta.rosetta.protocols.task_operations.ModifyAnnealerCreator method) (pyrosetta.rosetta.protocols.task_operations.MutationSetDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperation static method) (pyrosetta.rosetta.protocols.task_operations.pHVariantTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.PreventChainFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.PreventResiduesFromRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinCore static method) (pyrosetta.rosetta.protocols.task_operations.ProteinCoreFilterCreator method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.ProteinInterfaceDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperation static method) (pyrosetta.rosetta.protocols.task_operations.PruneBuriedUnsatsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDB static method) (pyrosetta.rosetta.protocols.task_operations.ReadResfileFromDBCreator method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperation static method) (pyrosetta.rosetta.protocols.task_operations.ResfileCommandOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperation static method) (pyrosetta.rosetta.protocols.task_operations.ResidueProbDesignOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilities static method) (pyrosetta.rosetta.protocols.task_operations.RestrictAAsFromProbabilitiesCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictByCalculatorsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictChainToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictConservedLowDdgOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesAtAlignedPositionsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictIdentitiesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictInterGroupVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictNativeResiduesOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictNonSurfaceToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictResiduesToRepackingOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToAlignedSegmentsOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3Loop static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToCDRH3LoopCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToInterfaceVectorOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToMoveMapChiOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToNeighborhoodOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperation static method) (pyrosetta.rosetta.protocols.task_operations.RestrictToTerminiOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperation static method) (pyrosetta.rosetta.protocols.task_operations.RetrieveStoredTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperation static method) (pyrosetta.rosetta.protocols.task_operations.SelectByDeltaScoreOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperation static method) (pyrosetta.rosetta.protocols.task_operations.SelectByDensityFitOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperation static method) (pyrosetta.rosetta.protocols.task_operations.SelectBySASAOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperation static method) (pyrosetta.rosetta.protocols.task_operations.SelectResiduesWithinChainOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperation static method) (pyrosetta.rosetta.protocols.task_operations.SeqprofConsensusOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperation static method) (pyrosetta.rosetta.protocols.task_operations.SequenceMotifTaskOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperation static method) (pyrosetta.rosetta.protocols.task_operations.SetIGTypeOperationCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreCombinedStoredTasksMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMover static method) (pyrosetta.rosetta.protocols.task_operations.StoreTaskMoverCreator method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation static method) (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperationCreator method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMover static method) (pyrosetta.rosetta.protocols.testing.BenchmarkBuildRotamersMoverCreator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGenerator static method) (pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators.trRosettaConstraintGeneratorCreator method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover static method) (pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMover static method) (pyrosetta.rosetta.protocols.vardist_solaccess.LoadVarSolDistSasaCalculatorMoverCreator method) provide_xml_schema_attributes() (pyrosetta.rosetta.core.pack.task.residue_selector.ClashBasedShellSelector static method) provide_xml_schema_with_name() (pyrosetta.rosetta.protocols.denovo_design.movers.BuildDeNovoBackboneMover static method) (pyrosetta.rosetta.protocols.denovo_design.movers.FoldArchitectMover static method) provide_xsd_information() (pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.Parameter method) (pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.RealVectorValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeValuedParameter method) (pyrosetta.rosetta.core.conformation.parametric.SizeVectorValuedParameter method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.OmegaBundleParameter method) proxy() (pyrosetta.rosetta.ObjexxFCL.FArray1_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray1_int_t method) 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(pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3A_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray4D_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray5D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_bool_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_1_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_2_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_3_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_4_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBDepScoreInterpData_5_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_BBIndNRChiSample_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_float_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray1D_int_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_FArray2D_float__star__t method) (pyrosetta.rosetta.ObjexxFCL.FArray_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_complex_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_string_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_char_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_unsigned_long_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.ObjexxFCL.FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t method) ProxySentinel (class in pyrosetta.rosetta.ObjexxFCL.internal) prune_cavity_balls() (in module pyrosetta.rosetta.core.scoring.packstat) prune_cavity_burial_probe_radii (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) prune_donor_acceptor_groups_lacking_hbonds_to_packable() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyNode method) prune_hidden_cavity_balls() (in module pyrosetta.rosetta.core.scoring.packstat) prune_max_delta (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) prune_max_iters (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) prune_small_bins() (pyrosetta.rosetta.core.scoring.motif.XformScore method) prune_voxels_for_fixed_residues() (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyVoxelGrid method) PruneBuriedUnsats_RotamerSetsOperation (class in pyrosetta.rosetta.protocols.task_operations) PruneBuriedUnsatsOperation (class in pyrosetta.rosetta.protocols.task_operations) PruneBuriedUnsatsOperationCreator (class in pyrosetta.rosetta.protocols.task_operations) prv_eqxyz() (pyrosetta.rosetta.protocols.md.CartesianMD method) (pyrosetta.rosetta.protocols.md.MDBase method) psc_compare() (in module pyrosetta.rosetta.core.pack.dunbrack) pSer2Asp_centroid (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) pSer2Glu_centroid (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) PSEUDO_PROTEIN (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid attribute) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid.PtType attribute) PseudoBond (class in pyrosetta.rosetta.core.conformation) (pyrosetta.rosetta.core.chemical.BondName attribute) PseudoBondCollection (class in pyrosetta.rosetta.core.conformation) PseudoBondOrder (pyrosetta.rosetta.core.chemical.BondOrder attribute) pseudobonds() (pyrosetta.rosetta.core.conformation.Residue method) PSEUDOCONTACT_SHIFT_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) PSEUDOCONTACT_SHIFT_MULTI_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) PseudocontactShiftEnergyController (class in pyrosetta.rosetta.protocols.topology_broker) PseudocontactShiftEnergyController_Ts1 (class in pyrosetta.rosetta.protocols.topology_broker) PseudocontactShiftEnergyController_Ts2 (class in pyrosetta.rosetta.protocols.topology_broker) PseudocontactShiftEnergyController_Ts3 (class in pyrosetta.rosetta.protocols.topology_broker) PseudocontactShiftEnergyController_Ts4 (class in pyrosetta.rosetta.protocols.topology_broker) PseudocontactShiftEnergyCreator (class in pyrosetta.rosetta.protocols.scoring.methods.pcs) PseudocontactShiftEnergyCreator_Ts1 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) PseudocontactShiftEnergyCreator_Ts2 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) PseudocontactShiftEnergyCreator_Ts3 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) PseudocontactShiftEnergyCreator_Ts4 (class in pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) pseudocount (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileConfig property) PseudoPerplexityMetric (class in pyrosetta.rosetta.protocols.esm_perplexity) PseudoPerplexityMetricCreator (class in pyrosetta.rosetta.protocols.esm_perplexity) pseudorotation() (pyrosetta.rosetta.protocols.dna.DNABase method) PSF_NEED_FULL_POSE_SET (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFlags attribute) PSF_NONE (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFlags attribute) Psi (class in pyrosetta.rosetta.protocols.frag_picker.scores) psi (pyrosetta.rosetta.core.fragment.torsions property) PSI (pyrosetta.rosetta.core.scoring.ProteinTorsion attribute) psi (pyrosetta.rosetta.protocols.indexed_structure_store.ResidueBackboneEntry property) (pyrosetta.rosetta.protocols.jumping.DisulfTemplate property) (pyrosetta.rosetta.protocols.jumping.PairingTemplate property) (pyrosetta.rosetta.protocols.pockets.spherical_coor_triplet property) (pyrosetta.rosetta.protocols.pockets.triplet_and_originnum property) psi() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.motif.Xfres method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.FreePeptide method) (pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.Residue method) (pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals method) (pyrosetta.rosetta.protocols.frag_picker.PhiPsiTalosIO method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) (pyrosetta.rosetta.protocols.frags.RMSVallData method) (pyrosetta.rosetta.protocols.frags.VallData method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.loophash.BackboneSegment method) (pyrosetta.rosetta.protocols.match.upstream.OriginalBackboneBuildPoint method) (pyrosetta.rosetta.protocols.match.upstream.ProteinBackboneBuildPoint method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptEPositionData method) (pyrosetta.rosetta.protocols.splice.BBDofs method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.MainChainTorsionSet method) psi_ (pyrosetta.rosetta.protocols.loop_grower.ResTorsions property) PSI_ATOM (pyrosetta.rosetta.core.chemical.GreekDistance attribute) psi_dihedral (pyrosetta.rosetta.core.id.MainchainTorsionType attribute) psi_index() (pyrosetta.rosetta.core.scoring.OmegaTether method) psi_max() (pyrosetta.rosetta.core.sequence.ABEGO method) psi_min() (pyrosetta.rosetta.core.sequence.ABEGO method) psipred2_confidence (pyrosetta.rosetta.core.io.external.PsiPredResult property) psipred_alpha_helix_prob_cutoff() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) psipred_assignment_file() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) psipred_assignment_file_contents() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) psipred_beta_strand_prob_cutoff() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) psipred_prob (pyrosetta.rosetta.core.io.external.PsiPredResult property) PsiPredInterface (class in pyrosetta.rosetta.core.io.external) PsiPredResult (class in pyrosetta.rosetta.core.io.external) psis (pyrosetta.rosetta.protocols.antibody.clusters.ClusterData property) PSM_append (pyrosetta.rosetta.protocols.cyclic_peptide.PSM_StubMode attribute) PSM_insert (pyrosetta.rosetta.protocols.cyclic_peptide.PSM_StubMode attribute) PSM_prepend (pyrosetta.rosetta.protocols.cyclic_peptide.PSM_StubMode attribute) PSM_StubMode (class in pyrosetta.rosetta.protocols.cyclic_peptide) psn (pyrosetta.rosetta.protocols.constel.ResMut property) PSSM2BfactorMover (class in pyrosetta.rosetta.protocols.simple_moves) PSSM2BfactorMoverCreator (class in pyrosetta.rosetta.protocols.simple_moves) pssm_() (pyrosetta.rosetta.protocols.protein_interface_design.ReportPSSMDifferences method) pssm_data (pyrosetta.rosetta.protocols.optimize_weights.OptEPositionDataType attribute) pssm_energy_at_frame_seqpos() (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) PSSMOptEPositionData (class in pyrosetta.rosetta.protocols.optimize_weights) Pt (pyrosetta.rosetta.core.chemical.element.Elements attribute) PT_angle (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_angle_vector (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_boolean (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_end_of_list (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_integer (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_integer_vector (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_natural_number (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_natural_number_vector (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_nonnegative_valued_real (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_nonnegative_valued_real_vector (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_positive_valued_real (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_positive_valued_real_vector (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_real (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_real_vector (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_whole_number (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_generic_whole_number_vector (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) PT_invalid_type (pyrosetta.rosetta.core.conformation.parametric.ParameterType attribute) ptask() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) ptm_mode() (pyrosetta.rosetta.protocols.ptm_prediction.PTMPredictionMetric method) PTMPredictionMetric (class in pyrosetta.rosetta.protocols.ptm_prediction) PTMPredictionMetric.PTMPredictionMetricModes (class in pyrosetta.rosetta.protocols.ptm_prediction) PTMPredictionMetricCreator (class in pyrosetta.rosetta.protocols.ptm_prediction) PTMPredictionTensorflowProtocol (class in pyrosetta.rosetta.protocols.ptm_prediction) PTMPredictionTensorflowProtocolBase (class in pyrosetta.rosetta.protocols.ptm_prediction) ptrCast() (pyrosetta.rosetta.RDKit.RDValue method) Pu (pyrosetta.rosetta.core.chemical.element.Elements attribute) pubimbue() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) public_array_to_private_data() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CentroidRotamerSampleData method) public_release() (pyrosetta.rosetta.utility.Version static method) pubseekoff() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) pubseekpos() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) pubsetbuf() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) pubsync() (pyrosetta.rosetta.std.filebuf method) (pyrosetta.rosetta.std.streambuf method) (pyrosetta.rosetta.std.stringbuf method) (pyrosetta.rosetta.std.wstreambuf method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_streambuf_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) pucker() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_SugarStepWiseSampler method) pucker_state() (pyrosetta.rosetta.protocols.stepwise.sampler.rna.RNA_ChiStepWiseSampler method) PuckerState (class in pyrosetta.rosetta.core.chemical.rna) pure_test_p() (pyrosetta.rosetta.utility.py.OverloadTest method) pure_test_ref() (pyrosetta.rosetta.utility.py.OverloadTest method) PURE_TOPO_RESAMPLING (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeCentroid.IterationStage attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom attribute) (pyrosetta.rosetta.protocols.abinitio.IterativeFullatom.IterationStage attribute) purge_missing_density() (pyrosetta.rosetta.protocols.pose_sewing.data_storage.TerminalDSSPSortedPoseVector method) PURINE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) push() (pyrosetta.rosetta.ObjexxFCL.internal.ObserverGraph method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareByScoreCombination_t method) (pyrosetta.rosetta.protocols.frag_picker.LazySortedVector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_protocols_frag_picker_CompareTotalScore_t method) (pyrosetta.rosetta.protocols.frag_picker.quota.ABEGO_SS_Pool method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaPool method) (pyrosetta.rosetta.protocols.frag_picker.quota.SecondaryStructurePool method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore method) (pyrosetta.rosetta.protocols.loop_grower.LoopComparator method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.std.priority_queue_protocols_motif_grafting_movers_MotifMatch_std_vector_protocols_motif_grafting_movers_MotifMatch_std_less_protocols_motif_grafting_movers_MotifMatch_t method) push_back() (pyrosetta.rosetta.core.conformation.PseudoBondCollection method) (pyrosetta.rosetta.core.id.SequenceMapping method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.pose.copydofs.CopyDofsInfo method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) (pyrosetta.rosetta.core.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.rna.RNA_Motifs method) (pyrosetta.rosetta.core.sequence.DerivedSequenceMapping method) (pyrosetta.rosetta.numeric.IntervalSet_Double method) (pyrosetta.rosetta.numeric.IntervalSet_double_t method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasedMonteCarlo method) (pyrosetta.rosetta.protocols.cluster.AssignToClustersMover method) (pyrosetta.rosetta.protocols.cluster.Cluster method) (pyrosetta.rosetta.protocols.cluster.ClusterBase method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_Loop method) (pyrosetta.rosetta.protocols.cluster.ClusterPhilStyle_PoseReporter method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints method) (pyrosetta.rosetta.protocols.cluster.EnsembleConstraints_Simple method) (pyrosetta.rosetta.protocols.cluster.GatherPosesMover method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.VectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.SheetSet method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.loops.LoopsFileData method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.monte_carlo.MonteCarloInterface method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.moves.ReplicaExchangeMC method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.rna.denovo.coarse.SourcePositions method) (pyrosetta.rosetta.protocols.splice.ResidueBBDofs method) (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.deep_copy_vector1_std_shared_ptr_core_chemical_Orbital_t method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyOptionKey_utility_options_VariantOption_utility_options_ScalarOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_AnyVectorOptionKey_utility_options_VariantOption_utility_options_VectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanOptionKey_utility_options_BooleanOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_BooleanVectorOptionKey_utility_options_BooleanVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileOptionKey_utility_options_FileOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_FileVectorOptionKey_utility_options_FileVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerOptionKey_utility_options_IntegerOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_IntegerVectorOptionKey_utility_options_IntegerVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_OptionKey_utility_options_OptionTypes_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathOptionKey_utility_options_PathOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_PathVectorOptionKey_utility_options_PathVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealOptionKey_utility_options_RealOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_RealVectorOptionKey_utility_options_RealVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_ResidueChainVectorOptionKey_utility_options_ResidueChainVectorOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringOptionKey_utility_options_StringOption_t method) (pyrosetta.rosetta.utility.keys.SmallKeyVector_utility_options_StringVectorOptionKey_utility_options_StringVectorOption_t method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_BooleanVectorOptionKey_bool_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_FileVectorOptionKey_utility_file_FileName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_IntegerVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_PathVectorOptionKey_utility_file_PathName_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_RealVectorOptionKey_double_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_ResidueChainVectorOptionKey_int_t method) (pyrosetta.rosetta.utility.options.VectorOption_T_utility_options_StringVectorOptionKey_std_string_t method) push_back_and_finalize() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) push_back_backbone() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) push_back_CA_xyz() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) push_back_CA_xyz_from_silent_file() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) push_back_raw() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) push_back_restorsions() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) push_back_sheet() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolution method) push_front() (pyrosetta.rosetta.protocols.cluster.Cluster method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue method) (pyrosetta.rosetta.protocols.wum.WorkUnitQueue_Swapped method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) push_job_to_front_of_queue() (pyrosetta.rosetta.protocols.jd3.job_distributors.JobExtractor method) push_node() (pyrosetta.rosetta.utility.tag.XMLErrorHandler method) push_passport() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) push_to_front_of_history_queue() (pyrosetta.rosetta.utility.recent_history_queue method) put() (pyrosetta.logging_support.PythonLoggingSink method) (pyrosetta.rosetta.basic.basic_otstream_char_std_char_traits_char_t method) (pyrosetta.rosetta.basic.ComparingTracer method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.TracerToFile method) (pyrosetta.rosetta.cppdb.backend.statements_cache method) (pyrosetta.rosetta.cppdb.pool method) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.ofstream method) (pyrosetta.rosetta.std.ostream method) (pyrosetta.rosetta.std.ostringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wostream method) (pyrosetta.rosetta.utility.io.mpi_stream.basic_mpi_ostream_char_std_char_traits_char_std_allocator_char_unsigned_char_std_allocator_unsigned_char_t method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) put_in_cutpoint() (in module pyrosetta.rosetta.core.import_pose) put_in_cutpoints() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.TransientCutpointHandler method) put_intra_into_total() (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) put_jump_stubs_intra_residue() (pyrosetta.rosetta.core.kinematics.FoldTree method) putback() (pyrosetta.rosetta.std.ifstream method) (pyrosetta.rosetta.std.iostream method) (pyrosetta.rosetta.std.istream method) (pyrosetta.rosetta.std.istringstream method) (pyrosetta.rosetta.std.stringstream method) (pyrosetta.rosetta.std.wistream method) (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) PValuedFragmentScoreManager (class in pyrosetta.rosetta.protocols.frag_picker.scores) pword() (pyrosetta.rosetta.std.ios_base method) Px (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) px() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) Py (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) py() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) Py_xyzTransform_double (class in pyrosetta.rosetta.numeric) PyEnergyMethodRegistrator (class in pyrosetta.rosetta.core.scoring.methods) PyExitCallback (class in pyrosetta.rosetta.utility.py) PyJobDistributor (class in pyrosetta.toolbox.py_jobdistributor) pymol() (pyrosetta.rosetta.protocols.moves.PyMOLObserver method) pymol_color_change() (pyrosetta.rosetta.protocols.docking.DockingLowRes method) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble method) pymol_name() (pyrosetta.rosetta.protocols.moves.PyMOLMover method) PYMOL_OBSERVER (pyrosetta.rosetta.core.pose.datacache.CacheableObserverType attribute) pymol_sel_hbond_unsat (pyrosetta.rosetta.protocols.analysis.InterfaceData property) pymol_sel_interface (pyrosetta.rosetta.protocols.analysis.InterfaceData property) pymol_sel_packing (pyrosetta.rosetta.protocols.analysis.InterfaceData property) PyMOLMover (class in pyrosetta.rosetta.protocols.moves) PyMOLMoverCreator (class in pyrosetta.rosetta.protocols.moves) PyMOLObserver (class in pyrosetta.rosetta.protocols.moves) PyMOLObserver.ObserverType (class in pyrosetta.rosetta.protocols.moves) PYRANOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) PyReturnValuePolicyTest_DummyClassCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_DummyClassOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_PoseCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_PoseOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_ScoreFunctionCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_ScoreFunctionCOP2() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_ScoreFunctionOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_SF_ReplicaCOP() (in module pyrosetta.rosetta.protocols.toolbox) PyReturnValuePolicyTest_SF_ReplicaOP() (in module pyrosetta.rosetta.protocols.toolbox) PYRIMIDINE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) pyrimidine_flip_trial() (pyrosetta.rosetta.protocols.rna.movers.ErraserMinimizerMover method) pyrosetta module pyrosetta.bindings module pyrosetta.bindings.energies module pyrosetta.bindings.homogeneous_transform module pyrosetta.bindings.pose module pyrosetta.bindings.rt module pyrosetta.bindings.utility module pyrosetta.distributed module pyrosetta.distributed.dask module pyrosetta.distributed.docs module pyrosetta.distributed.io module pyrosetta.distributed.packed_pose module pyrosetta.distributed.packed_pose.core module pyrosetta.distributed.tasks module pyrosetta.distributed.utility module pyrosetta.distributed.utility.pickle module pyrosetta.io module pyrosetta.io.silent_file_map module pyrosetta.logging_support module pyrosetta.network module pyrosetta.network.rosetta_udp_to_tcp_bridge module pyrosetta.numeric module pyrosetta.numeric.alignment module pyrosetta.protocols module pyrosetta.protocols.h5_fragment_store_provider module pyrosetta.protocols.h5_importer module pyrosetta.protocols.h5_structure_store_provider module pyrosetta.rosetta module pyrosetta.rosetta.basic module pyrosetta.rosetta.basic.citation_manager module pyrosetta.rosetta.basic.database module pyrosetta.rosetta.basic.database.insert_statement_generator module pyrosetta.rosetta.basic.database.schema_generator module pyrosetta.rosetta.basic.datacache module pyrosetta.rosetta.basic.gpu module pyrosetta.rosetta.basic.mpi module pyrosetta.rosetta.basic.options module pyrosetta.rosetta.basic.random module pyrosetta.rosetta.basic.resource_manager module pyrosetta.rosetta.basic.resource_manager.locator module pyrosetta.rosetta.basic.sampling module pyrosetta.rosetta.basic.sampling.orientations module pyrosetta.rosetta.basic.svd module pyrosetta.rosetta.basic.tensorflow_manager module pyrosetta.rosetta.basic.thread_manager module pyrosetta.rosetta.core module pyrosetta.rosetta.core.chemical module pyrosetta.rosetta.core.chemical.bcl module pyrosetta.rosetta.core.chemical.carbohydrates module pyrosetta.rosetta.core.chemical.element module pyrosetta.rosetta.core.chemical.gasteiger module pyrosetta.rosetta.core.chemical.io module pyrosetta.rosetta.core.chemical.mainchain_potential module pyrosetta.rosetta.core.chemical.mmCIF module pyrosetta.rosetta.core.chemical.modifications module pyrosetta.rosetta.core.chemical.NucleotideTools module pyrosetta.rosetta.core.chemical.orbitals module pyrosetta.rosetta.core.chemical.rdkit module pyrosetta.rosetta.core.chemical.rings module pyrosetta.rosetta.core.chemical.rna module pyrosetta.rosetta.core.chemical.rotamers module pyrosetta.rosetta.core.chemical.sdf module pyrosetta.rosetta.core.conformation module pyrosetta.rosetta.core.conformation.carbohydrates module pyrosetta.rosetta.core.conformation.membrane module pyrosetta.rosetta.core.conformation.membrane.membrane_geometry module pyrosetta.rosetta.core.conformation.orbitals module pyrosetta.rosetta.core.conformation.parametric module pyrosetta.rosetta.core.conformation.residue_datacache module pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType module pyrosetta.rosetta.core.conformation.signals module pyrosetta.rosetta.core.conformation.symmetry module pyrosetta.rosetta.core.energy_methods module pyrosetta.rosetta.core.energy_methods.dfire module pyrosetta.rosetta.core.environment module pyrosetta.rosetta.core.enzymes module pyrosetta.rosetta.core.fragment module pyrosetta.rosetta.core.fragment.picking_old module pyrosetta.rosetta.core.fragment.picking_old.concepts module pyrosetta.rosetta.core.fragment.picking_old.vall module pyrosetta.rosetta.core.fragment.picking_old.vall.eval module pyrosetta.rosetta.core.fragment.picking_old.vall.gen module pyrosetta.rosetta.core.fragment.picking_old.vall.scores module pyrosetta.rosetta.core.fragment.rna module pyrosetta.rosetta.core.grid module pyrosetta.rosetta.core.id module pyrosetta.rosetta.core.import_pose module pyrosetta.rosetta.core.import_pose.atom_tree_diffs module pyrosetta.rosetta.core.import_pose.libraries module pyrosetta.rosetta.core.import_pose.options module pyrosetta.rosetta.core.import_pose.pose_stream module pyrosetta.rosetta.core.init module pyrosetta.rosetta.core.io module pyrosetta.rosetta.core.io.carbohydrates module pyrosetta.rosetta.core.io.external module pyrosetta.rosetta.core.io.mmcif module pyrosetta.rosetta.core.io.mmtf module pyrosetta.rosetta.core.io.nmr module pyrosetta.rosetta.core.io.pdb module pyrosetta.rosetta.core.io.pose_from_sfr module pyrosetta.rosetta.core.io.pose_to_sfr module pyrosetta.rosetta.core.io.PositionDdGInfo module pyrosetta.rosetta.core.io.raw_data module pyrosetta.rosetta.core.io.rcsb module pyrosetta.rosetta.core.io.rna module pyrosetta.rosetta.core.io.sequence_comparation module pyrosetta.rosetta.core.io.serialization module pyrosetta.rosetta.core.io.silent module pyrosetta.rosetta.core.kinematics module pyrosetta.rosetta.core.kinematics.inverse module pyrosetta.rosetta.core.kinematics.jacobian module pyrosetta.rosetta.core.kinematics.tree module pyrosetta.rosetta.core.membrane module pyrosetta.rosetta.core.optimization module pyrosetta.rosetta.core.optimization.symmetry module pyrosetta.rosetta.core.pack module pyrosetta.rosetta.core.pack.annealer module pyrosetta.rosetta.core.pack.dunbrack module pyrosetta.rosetta.core.pack.dunbrack.cenrot module pyrosetta.rosetta.core.pack.guidance_scoreterms module pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty module pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty module pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph module pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy module pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome module pyrosetta.rosetta.core.pack.guidance_scoreterms.sap module pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy module pyrosetta.rosetta.core.pack.hbonds module pyrosetta.rosetta.core.pack.interaction_graph module pyrosetta.rosetta.core.pack.palette module pyrosetta.rosetta.core.pack.rotamer_set module pyrosetta.rosetta.core.pack.rotamer_set.symmetry module pyrosetta.rosetta.core.pack.rotamers module pyrosetta.rosetta.core.pack.scmin module pyrosetta.rosetta.core.pack.task module pyrosetta.rosetta.core.pack.task.operation module pyrosetta.rosetta.core.pack.task.residue_selector module pyrosetta.rosetta.core.pack.task.rna module pyrosetta.rosetta.core.pack_basic module pyrosetta.rosetta.core.pose module pyrosetta.rosetta.core.pose.carbohydrates module pyrosetta.rosetta.core.pose.copydofs module pyrosetta.rosetta.core.pose.datacache module pyrosetta.rosetta.core.pose.full_model_info module pyrosetta.rosetta.core.pose.metrics module pyrosetta.rosetta.core.pose.metrics.simple_calculators module pyrosetta.rosetta.core.pose.motif module pyrosetta.rosetta.core.pose.ncbb module pyrosetta.rosetta.core.pose.reference_pose module pyrosetta.rosetta.core.pose.rna module pyrosetta.rosetta.core.pose.rna.secstruct_legacy module pyrosetta.rosetta.core.pose.signals module pyrosetta.rosetta.core.pose.symmetry module pyrosetta.rosetta.core.pose.toolbox module pyrosetta.rosetta.core.scoring module pyrosetta.rosetta.core.scoring.aa_composition_energy module pyrosetta.rosetta.core.scoring.annealing module pyrosetta.rosetta.core.scoring.atomic_depth module pyrosetta.rosetta.core.scoring.bin_transitions module pyrosetta.rosetta.core.scoring.carbohydrates module pyrosetta.rosetta.core.scoring.carbon_hbonds module pyrosetta.rosetta.core.scoring.constraints module pyrosetta.rosetta.core.scoring.cryst module pyrosetta.rosetta.core.scoring.custom_pair_distance module pyrosetta.rosetta.core.scoring.disulfides module pyrosetta.rosetta.core.scoring.dna module pyrosetta.rosetta.core.scoring.dssp module pyrosetta.rosetta.core.scoring.elec module pyrosetta.rosetta.core.scoring.elec.electrie module pyrosetta.rosetta.core.scoring.electron_density module pyrosetta.rosetta.core.scoring.electron_density_atomwise module pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType module pyrosetta.rosetta.core.scoring.epr_deer module pyrosetta.rosetta.core.scoring.epr_deer.metrics module pyrosetta.rosetta.core.scoring.etable module pyrosetta.rosetta.core.scoring.etable.coulomb module pyrosetta.rosetta.core.scoring.etable.count_pair module pyrosetta.rosetta.core.scoring.etable.etrie module pyrosetta.rosetta.core.scoring.facts module pyrosetta.rosetta.core.scoring.fiber_diffraction module pyrosetta.rosetta.core.scoring.func module pyrosetta.rosetta.core.scoring.geometric_solvation module pyrosetta.rosetta.core.scoring.hbonds module pyrosetta.rosetta.core.scoring.hbonds.graph module pyrosetta.rosetta.core.scoring.hbonds.hbtrie module pyrosetta.rosetta.core.scoring.interface_ module pyrosetta.rosetta.core.scoring.lkball module pyrosetta.rosetta.core.scoring.lkball.lkbtrie module pyrosetta.rosetta.core.scoring.loop_graph module pyrosetta.rosetta.core.scoring.loop_graph.evaluator module pyrosetta.rosetta.core.scoring.magnesium module pyrosetta.rosetta.core.scoring.membrane module pyrosetta.rosetta.core.scoring.methods module pyrosetta.rosetta.core.scoring.methods.dfire module pyrosetta.rosetta.core.scoring.mhc_epitope_energy module pyrosetta.rosetta.core.scoring.mm module pyrosetta.rosetta.core.scoring.mm.mmtrie module pyrosetta.rosetta.core.scoring.motif module pyrosetta.rosetta.core.scoring.netcharge_energy module pyrosetta.rosetta.core.scoring.nmr module pyrosetta.rosetta.core.scoring.nmr.pcs module pyrosetta.rosetta.core.scoring.nmr.pre module pyrosetta.rosetta.core.scoring.nmr.rdc module pyrosetta.rosetta.core.scoring.nv module pyrosetta.rosetta.core.scoring.orbitals module pyrosetta.rosetta.core.scoring.packing module pyrosetta.rosetta.core.scoring.packstat module pyrosetta.rosetta.core.scoring.packstat.old module pyrosetta.rosetta.core.scoring.power_diagram module pyrosetta.rosetta.core.scoring.rna module pyrosetta.rosetta.core.scoring.rna.chemical_shift module pyrosetta.rosetta.core.scoring.rna.data module pyrosetta.rosetta.core.scoring.sasa module pyrosetta.rosetta.core.scoring.saxs module pyrosetta.rosetta.core.scoring.sc module pyrosetta.rosetta.core.scoring.solid_surface module pyrosetta.rosetta.core.scoring.sym_e module pyrosetta.rosetta.core.scoring.symmetry module pyrosetta.rosetta.core.scoring.trie module pyrosetta.rosetta.core.scoring.vdwaals module pyrosetta.rosetta.core.select module pyrosetta.rosetta.core.select.jump_selector module pyrosetta.rosetta.core.select.movemap module pyrosetta.rosetta.core.select.residue_selector module pyrosetta.rosetta.core.select.residue_selector.slice_enums module pyrosetta.rosetta.core.select.util module pyrosetta.rosetta.core.sequence module pyrosetta.rosetta.core.simple_metrics module pyrosetta.rosetta.core.simple_metrics.composite_metrics module pyrosetta.rosetta.core.simple_metrics.metrics module pyrosetta.rosetta.core.simple_metrics.per_residue_metrics module pyrosetta.rosetta.core.util module pyrosetta.rosetta.cppdb module pyrosetta.rosetta.cppdb.backend module pyrosetta.rosetta.numeric module pyrosetta.rosetta.numeric.alignment module pyrosetta.rosetta.numeric.conversions module pyrosetta.rosetta.numeric.crick_equations module pyrosetta.rosetta.numeric.expression_parser module pyrosetta.rosetta.numeric.fourier module pyrosetta.rosetta.numeric.geometry module pyrosetta.rosetta.numeric.geometry.hashing module pyrosetta.rosetta.numeric.histograms module pyrosetta.rosetta.numeric.interpolation module pyrosetta.rosetta.numeric.interpolation.spline module pyrosetta.rosetta.numeric.kdtree module pyrosetta.rosetta.numeric.kinematic_closure module pyrosetta.rosetta.numeric.kinematic_closure.radians module pyrosetta.rosetta.numeric.linear_algebra module pyrosetta.rosetta.numeric.model_quality module pyrosetta.rosetta.numeric.nls module pyrosetta.rosetta.numeric.random module pyrosetta.rosetta.numeric.statistics module pyrosetta.rosetta.ObjexxFCL module pyrosetta.rosetta.ObjexxFCL.bit module pyrosetta.rosetta.ObjexxFCL.format module pyrosetta.rosetta.ObjexxFCL.Fortran module pyrosetta.rosetta.ObjexxFCL.internal module pyrosetta.rosetta.ObjexxFCL.internal.ObserverMediator module pyrosetta.rosetta.protocols module pyrosetta.rosetta.protocols.aa_composition module pyrosetta.rosetta.protocols.abinitio module pyrosetta.rosetta.protocols.abinitio.abscript module pyrosetta.rosetta.protocols.analysis module pyrosetta.rosetta.protocols.analysis.burial_metrics module pyrosetta.rosetta.protocols.analysis.simple_metrics module pyrosetta.rosetta.protocols.anchored_design module pyrosetta.rosetta.protocols.antibody module pyrosetta.rosetta.protocols.antibody.clusters module pyrosetta.rosetta.protocols.antibody.constraints module pyrosetta.rosetta.protocols.antibody.design module pyrosetta.rosetta.protocols.antibody.grafting module pyrosetta.rosetta.protocols.antibody.residue_selector module pyrosetta.rosetta.protocols.antibody.snugdock module pyrosetta.rosetta.protocols.antibody.task_operations module pyrosetta.rosetta.protocols.antibody_legacy module pyrosetta.rosetta.protocols.backbone_moves module pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover module pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers module pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.gap_solution_pickers module pyrosetta.rosetta.protocols.backrub module pyrosetta.rosetta.protocols.branch_angle module pyrosetta.rosetta.protocols.buns module pyrosetta.rosetta.protocols.calc_taskop_filters module pyrosetta.rosetta.protocols.calc_taskop_movers module pyrosetta.rosetta.protocols.canonical_sampling module pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks module pyrosetta.rosetta.protocols.carbohydrates module pyrosetta.rosetta.protocols.cartesian module pyrosetta.rosetta.protocols.checkpoint module pyrosetta.rosetta.protocols.chemically_conjugated_docking module pyrosetta.rosetta.protocols.chemistries module pyrosetta.rosetta.protocols.chromophore module pyrosetta.rosetta.protocols.cluster module pyrosetta.rosetta.protocols.cluster.calibur module pyrosetta.rosetta.protocols.comparative_modeling module pyrosetta.rosetta.protocols.comparative_modeling.features module pyrosetta.rosetta.protocols.constel module pyrosetta.rosetta.protocols.constraint_filters module pyrosetta.rosetta.protocols.constraint_generator module pyrosetta.rosetta.protocols.constraint_movers module pyrosetta.rosetta.protocols.constraints_additional module pyrosetta.rosetta.protocols.contact_map module pyrosetta.rosetta.protocols.coupled_moves module pyrosetta.rosetta.protocols.cryst module pyrosetta.rosetta.protocols.cutoutdomain module pyrosetta.rosetta.protocols.cyclic_peptide module pyrosetta.rosetta.protocols.cyclic_peptide.crosslinker module pyrosetta.rosetta.protocols.cyclic_peptide_predict module pyrosetta.rosetta.protocols.ddG module pyrosetta.rosetta.protocols.ddg module pyrosetta.rosetta.protocols.ddg.CartesianddG module pyrosetta.rosetta.protocols.denovo_design module pyrosetta.rosetta.protocols.denovo_design.architects module pyrosetta.rosetta.protocols.denovo_design.calculators module pyrosetta.rosetta.protocols.denovo_design.components module pyrosetta.rosetta.protocols.denovo_design.connection module pyrosetta.rosetta.protocols.denovo_design.constraints module pyrosetta.rosetta.protocols.denovo_design.filters module pyrosetta.rosetta.protocols.denovo_design.movers module pyrosetta.rosetta.protocols.denovo_design.residue_selectors module pyrosetta.rosetta.protocols.denovo_design.task_operations module pyrosetta.rosetta.protocols.design_opt module pyrosetta.rosetta.protocols.dna module pyrosetta.rosetta.protocols.dna_dock module pyrosetta.rosetta.protocols.docking module pyrosetta.rosetta.protocols.docking.membrane module pyrosetta.rosetta.protocols.docking.stateless module pyrosetta.rosetta.protocols.domain_assembly module pyrosetta.rosetta.protocols.drug_design module pyrosetta.rosetta.protocols.drug_design.bcl module pyrosetta.rosetta.protocols.electron_density module pyrosetta.rosetta.protocols.energy_based_clustering module pyrosetta.rosetta.protocols.environment module pyrosetta.rosetta.protocols.environment.claims module pyrosetta.rosetta.protocols.enzdes module pyrosetta.rosetta.protocols.enzdes.enzutil module pyrosetta.rosetta.protocols.enzymatic_movers module pyrosetta.rosetta.protocols.esm_perplexity module pyrosetta.rosetta.protocols.evaluation module pyrosetta.rosetta.protocols.evolution module pyrosetta.rosetta.protocols.evolution.AlignmentCleanerTools module pyrosetta.rosetta.protocols.farnesyl module pyrosetta.rosetta.protocols.features module pyrosetta.rosetta.protocols.features.helixAssembly module pyrosetta.rosetta.protocols.features.RelevantResiduesMode module pyrosetta.rosetta.protocols.features.strand_assembly module pyrosetta.rosetta.protocols.fibril module pyrosetta.rosetta.protocols.filters module pyrosetta.rosetta.protocols.fldsgn module pyrosetta.rosetta.protocols.fldsgn.filters module pyrosetta.rosetta.protocols.fldsgn.potentials module pyrosetta.rosetta.protocols.fldsgn.potentials.sspot module pyrosetta.rosetta.protocols.fldsgn.topology module pyrosetta.rosetta.protocols.flexpack module pyrosetta.rosetta.protocols.flexpack.annealer module pyrosetta.rosetta.protocols.flexpack.interaction_graph module pyrosetta.rosetta.protocols.flexpack.rotamer_set module pyrosetta.rosetta.protocols.flexpep_docking module pyrosetta.rosetta.protocols.floppy_tail module pyrosetta.rosetta.protocols.flxbb module pyrosetta.rosetta.protocols.fold_from_loops module pyrosetta.rosetta.protocols.fold_from_loops.constraint_generator module pyrosetta.rosetta.protocols.fold_from_loops.filters module pyrosetta.rosetta.protocols.fold_from_loops.movers module pyrosetta.rosetta.protocols.fold_from_loops.selectors module pyrosetta.rosetta.protocols.fold_from_loops.utils module pyrosetta.rosetta.protocols.forge module pyrosetta.rosetta.protocols.forge.build module pyrosetta.rosetta.protocols.forge.build.BuildInstructionState module pyrosetta.rosetta.protocols.forge.build.SegmentInsertConnectionScheme module pyrosetta.rosetta.protocols.forge.components module pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage module pyrosetta.rosetta.protocols.forge.constraints module pyrosetta.rosetta.protocols.forge.methods module pyrosetta.rosetta.protocols.forge.remodel module pyrosetta.rosetta.protocols.frag_picker module pyrosetta.rosetta.protocols.frag_picker.quota module pyrosetta.rosetta.protocols.frag_picker.scores module pyrosetta.rosetta.protocols.frags module pyrosetta.rosetta.protocols.generalized_kinematic_closure module pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter module pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber module pyrosetta.rosetta.protocols.generalized_kinematic_closure.selector module pyrosetta.rosetta.protocols.genetic_algorithm module pyrosetta.rosetta.protocols.geometry module pyrosetta.rosetta.protocols.glycan_docking module pyrosetta.rosetta.protocols.glycopeptide_docking module pyrosetta.rosetta.protocols.grafting module pyrosetta.rosetta.protocols.grafting.simple_movers module pyrosetta.rosetta.protocols.hbnet module pyrosetta.rosetta.protocols.helical_bundle module pyrosetta.rosetta.protocols.helical_bundle.parameters module pyrosetta.rosetta.protocols.helical_bundle_predict module pyrosetta.rosetta.protocols.helix_capper module pyrosetta.rosetta.protocols.hotspot_hashing module pyrosetta.rosetta.protocols.hotspot_hashing.movers module pyrosetta.rosetta.protocols.hybridization module pyrosetta.rosetta.protocols.hydrate module pyrosetta.rosetta.protocols.idealize module pyrosetta.rosetta.protocols.indel module pyrosetta.rosetta.protocols.indexed_structure_store module pyrosetta.rosetta.protocols.indexed_structure_store.filters module pyrosetta.rosetta.protocols.indexed_structure_store.movers module pyrosetta.rosetta.protocols.indexed_structure_store.search module pyrosetta.rosetta.protocols.init module pyrosetta.rosetta.protocols.interface module pyrosetta.rosetta.protocols.jd2 module pyrosetta.rosetta.protocols.jd2.archive module pyrosetta.rosetta.protocols.jd2.JobInputterInputSource module pyrosetta.rosetta.protocols.jd3 module pyrosetta.rosetta.protocols.jd3.chunk_library module pyrosetta.rosetta.protocols.jd3.chunk_library_inputters module pyrosetta.rosetta.protocols.jd3.dag_node_managers module pyrosetta.rosetta.protocols.jd3.deallocation module pyrosetta.rosetta.protocols.jd3.full_model module pyrosetta.rosetta.protocols.jd3.full_model_inputters module pyrosetta.rosetta.protocols.jd3.job_distributors module pyrosetta.rosetta.protocols.jd3.job_results module pyrosetta.rosetta.protocols.jd3.job_summaries module pyrosetta.rosetta.protocols.jd3.jobs module pyrosetta.rosetta.protocols.jd3.output module pyrosetta.rosetta.protocols.jd3.pose_inputters module pyrosetta.rosetta.protocols.jd3.pose_outputters module pyrosetta.rosetta.protocols.jd3.standard module pyrosetta.rosetta.protocols.jobdist module pyrosetta.rosetta.protocols.jumping module pyrosetta.rosetta.protocols.kinematic_closure module pyrosetta.rosetta.protocols.kinematic_closure.perturbers module pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers module pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers module pyrosetta.rosetta.protocols.kinmatch module pyrosetta.rosetta.protocols.legacy_sewing module pyrosetta.rosetta.protocols.legacy_sewing.sampling module pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements module pyrosetta.rosetta.protocols.legacy_sewing.scoring module pyrosetta.rosetta.protocols.ligand_docking module pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock module pyrosetta.rosetta.protocols.ligand_docking.ligand_options module pyrosetta.rosetta.protocols.ligand_docking.rdf module pyrosetta.rosetta.protocols.loop_build module pyrosetta.rosetta.protocols.loop_grower module pyrosetta.rosetta.protocols.loop_modeler module pyrosetta.rosetta.protocols.loop_modeler.perturbers module pyrosetta.rosetta.protocols.loop_modeling module pyrosetta.rosetta.protocols.loop_modeling.refiners module pyrosetta.rosetta.protocols.loop_modeling.samplers module pyrosetta.rosetta.protocols.loop_modeling.utilities module pyrosetta.rosetta.protocols.loophash module pyrosetta.rosetta.protocols.loops module pyrosetta.rosetta.protocols.loops.filters module pyrosetta.rosetta.protocols.loops.loop_closure module pyrosetta.rosetta.protocols.loops.loop_closure.ccd module pyrosetta.rosetta.protocols.loops.loop_closure.jacobi module pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure module pyrosetta.rosetta.protocols.loops.loop_mover module pyrosetta.rosetta.protocols.loops.loop_mover.perturb module pyrosetta.rosetta.protocols.loops.loop_mover.refine module pyrosetta.rosetta.protocols.loops.loops_definers module pyrosetta.rosetta.protocols.magnesium module pyrosetta.rosetta.protocols.mainchain_potential module pyrosetta.rosetta.protocols.make_rot_lib module pyrosetta.rosetta.protocols.match module pyrosetta.rosetta.protocols.match.downstream module pyrosetta.rosetta.protocols.match.output module pyrosetta.rosetta.protocols.match.upstream module pyrosetta.rosetta.protocols.matdes module pyrosetta.rosetta.protocols.md module pyrosetta.rosetta.protocols.mean_field module pyrosetta.rosetta.protocols.medal module pyrosetta.rosetta.protocols.membrane module pyrosetta.rosetta.protocols.membrane.benchmark module pyrosetta.rosetta.protocols.membrane.geometry module pyrosetta.rosetta.protocols.membrane.scoring module pyrosetta.rosetta.protocols.membrane.symmetry module pyrosetta.rosetta.protocols.membrane.visualize module pyrosetta.rosetta.protocols.membrane_benchmark module pyrosetta.rosetta.protocols.metal_interface module pyrosetta.rosetta.protocols.minimization_packing module pyrosetta.rosetta.protocols.minimization_packing.symmetry module pyrosetta.rosetta.protocols.monte_carlo module pyrosetta.rosetta.protocols.motif_grafting module pyrosetta.rosetta.protocols.motif_grafting.movers module pyrosetta.rosetta.protocols.motifs module pyrosetta.rosetta.protocols.moves module pyrosetta.rosetta.protocols.mpi_refinement module pyrosetta.rosetta.protocols.multistage_rosetta_scripts module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster module pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.metrics module pyrosetta.rosetta.protocols.multistate_design module pyrosetta.rosetta.protocols.ncbb module pyrosetta.rosetta.protocols.ncbb.oop module pyrosetta.rosetta.protocols.neighbor module pyrosetta.rosetta.protocols.network module pyrosetta.rosetta.protocols.nmr module pyrosetta.rosetta.protocols.nmr.pcs module pyrosetta.rosetta.protocols.nmr.pre module pyrosetta.rosetta.protocols.nmr.rdc module pyrosetta.rosetta.protocols.noesy_assign module pyrosetta.rosetta.protocols.normalmode module pyrosetta.rosetta.protocols.optimize_weights module pyrosetta.rosetta.protocols.pack_daemon module pyrosetta.rosetta.protocols.pack_interface module pyrosetta.rosetta.protocols.parser module pyrosetta.rosetta.protocols.pb_potential module pyrosetta.rosetta.protocols.pdbinfo_manipulations module pyrosetta.rosetta.protocols.peptide_deriver module pyrosetta.rosetta.protocols.pmut_scan module pyrosetta.rosetta.protocols.pockets module pyrosetta.rosetta.protocols.pose_creation module pyrosetta.rosetta.protocols.pose_length_moves module pyrosetta.rosetta.protocols.pose_metric_calculators module pyrosetta.rosetta.protocols.pose_reporters module pyrosetta.rosetta.protocols.pose_selectors module pyrosetta.rosetta.protocols.pose_sewing module pyrosetta.rosetta.protocols.pose_sewing.data_storage module pyrosetta.rosetta.protocols.pose_sewing.filters module pyrosetta.rosetta.protocols.pose_sewing.movers module pyrosetta.rosetta.protocols.pose_sewing.simple_metrics module pyrosetta.rosetta.protocols.protein_interface_design module pyrosetta.rosetta.protocols.protein_interface_design.filters module pyrosetta.rosetta.protocols.protein_interface_design.movers module pyrosetta.rosetta.protocols.protein_mpnn module pyrosetta.rosetta.protocols.ptm_prediction module pyrosetta.rosetta.protocols.qsar module pyrosetta.rosetta.protocols.qsar.scoring_grid module pyrosetta.rosetta.protocols.quantum_annealing module pyrosetta.rosetta.protocols.rbsegment_relax module pyrosetta.rosetta.protocols.recces module pyrosetta.rosetta.protocols.recces.options module pyrosetta.rosetta.protocols.recces.params module pyrosetta.rosetta.protocols.recces.sampler module pyrosetta.rosetta.protocols.recces.sampler.rna module pyrosetta.rosetta.protocols.recces.scratch module pyrosetta.rosetta.protocols.recon_design module pyrosetta.rosetta.protocols.relax module pyrosetta.rosetta.protocols.relax.loop module pyrosetta.rosetta.protocols.relax.membrane module pyrosetta.rosetta.protocols.residue_optimization module pyrosetta.rosetta.protocols.residue_selectors module pyrosetta.rosetta.protocols.rigid module pyrosetta.rosetta.protocols.rna module pyrosetta.rosetta.protocols.rna.denovo module pyrosetta.rosetta.protocols.rna.denovo.coarse module pyrosetta.rosetta.protocols.rna.denovo.movers module pyrosetta.rosetta.protocols.rna.denovo.output module pyrosetta.rosetta.protocols.rna.movers module pyrosetta.rosetta.protocols.rna.setup module pyrosetta.rosetta.protocols.rosetta_scripts module pyrosetta.rosetta.protocols.rotamer_recovery module pyrosetta.rosetta.protocols.RotamerDump module pyrosetta.rosetta.protocols.rpc module pyrosetta.rosetta.protocols.sasa_scores module pyrosetta.rosetta.protocols.score_filters module pyrosetta.rosetta.protocols.scoring module pyrosetta.rosetta.protocols.scoring.methods module pyrosetta.rosetta.protocols.scoring.methods.pcs module pyrosetta.rosetta.protocols.scoring.methods.pcs2 module pyrosetta.rosetta.protocols.scoring.methods.pcsTs1 module pyrosetta.rosetta.protocols.scoring.methods.pcsTs2 module pyrosetta.rosetta.protocols.scoring.methods.pcsTs3 module pyrosetta.rosetta.protocols.scoring.methods.pcsTs4 module pyrosetta.rosetta.protocols.scoring.methods.saxs module pyrosetta.rosetta.protocols.seeded_abinitio module pyrosetta.rosetta.protocols.sewing module pyrosetta.rosetta.protocols.sewing.data_storage module pyrosetta.rosetta.protocols.sewing.hashing module pyrosetta.rosetta.protocols.sewing.movers module pyrosetta.rosetta.protocols.sewing.requirements module pyrosetta.rosetta.protocols.sewing.scoring module pyrosetta.rosetta.protocols.sic_dock module pyrosetta.rosetta.protocols.sic_dock.scores module pyrosetta.rosetta.protocols.simple_ddg module pyrosetta.rosetta.protocols.simple_filters module pyrosetta.rosetta.protocols.simple_moves module pyrosetta.rosetta.protocols.simple_moves.a3b_hbs module pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock module pyrosetta.rosetta.protocols.simple_moves.bb_sampler module pyrosetta.rosetta.protocols.simple_moves.bin_transitions module pyrosetta.rosetta.protocols.simple_moves.chiral module pyrosetta.rosetta.protocols.simple_moves.hbs module pyrosetta.rosetta.protocols.simple_moves.oop module pyrosetta.rosetta.protocols.simple_moves.rational_mc module pyrosetta.rosetta.protocols.simple_moves.sidechain_moves module pyrosetta.rosetta.protocols.simple_moves.triazolamer module pyrosetta.rosetta.protocols.simple_pose_metric_calculators module pyrosetta.rosetta.protocols.simple_task_operations module pyrosetta.rosetta.protocols.sparta module pyrosetta.rosetta.protocols.splice module pyrosetta.rosetta.protocols.ss_prediction module pyrosetta.rosetta.protocols.star module pyrosetta.rosetta.protocols.stepwise module pyrosetta.rosetta.protocols.stepwise.legacy module pyrosetta.rosetta.protocols.stepwise.legacy.modeler module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.protein module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna module pyrosetta.rosetta.protocols.stepwise.legacy.screener module pyrosetta.rosetta.protocols.stepwise.modeler module pyrosetta.rosetta.protocols.stepwise.modeler.align module pyrosetta.rosetta.protocols.stepwise.modeler.movemap module pyrosetta.rosetta.protocols.stepwise.modeler.options module pyrosetta.rosetta.protocols.stepwise.modeler.packer module pyrosetta.rosetta.protocols.stepwise.modeler.polar_hydrogens module pyrosetta.rosetta.protocols.stepwise.modeler.precomputed module pyrosetta.rosetta.protocols.stepwise.modeler.protein module pyrosetta.rosetta.protocols.stepwise.modeler.protein.checker module pyrosetta.rosetta.protocols.stepwise.modeler.protein.loop_close module pyrosetta.rosetta.protocols.stepwise.modeler.rna module pyrosetta.rosetta.protocols.stepwise.modeler.rna.bulge module pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker module pyrosetta.rosetta.protocols.stepwise.modeler.rna.o2prime module pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate module pyrosetta.rosetta.protocols.stepwise.modeler.rna.rigid_body module pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters module pyrosetta.rosetta.protocols.stepwise.monte_carlo module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover module pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options module pyrosetta.rosetta.protocols.stepwise.monte_carlo.options module pyrosetta.rosetta.protocols.stepwise.monte_carlo.rna module pyrosetta.rosetta.protocols.stepwise.monte_carlo.submotif module pyrosetta.rosetta.protocols.stepwise.options module pyrosetta.rosetta.protocols.stepwise.sampler module pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs module pyrosetta.rosetta.protocols.stepwise.sampler.input_streams module pyrosetta.rosetta.protocols.stepwise.sampler.jump module pyrosetta.rosetta.protocols.stepwise.sampler.protein module pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body module pyrosetta.rosetta.protocols.stepwise.sampler.rna module pyrosetta.rosetta.protocols.stepwise.sampler.screener module pyrosetta.rosetta.protocols.stepwise.screener module pyrosetta.rosetta.protocols.stepwise.setup module pyrosetta.rosetta.protocols.struct_fragment module pyrosetta.rosetta.protocols.surface_docking module pyrosetta.rosetta.protocols.switches module pyrosetta.rosetta.protocols.symmetric_docking module pyrosetta.rosetta.protocols.symmetric_docking.membrane module pyrosetta.rosetta.protocols.symmetry module pyrosetta.rosetta.protocols.task_operations module pyrosetta.rosetta.protocols.tcr module pyrosetta.rosetta.protocols.testing module pyrosetta.rosetta.protocols.toolbox module pyrosetta.rosetta.protocols.toolbox.match_enzdes_util module pyrosetta.rosetta.protocols.toolbox.pose_manipulation module pyrosetta.rosetta.protocols.toolbox.py_inheritance_test module pyrosetta.rosetta.protocols.toolbox.rigid_body module pyrosetta.rosetta.protocols.toolbox.rotamer_set_operations module pyrosetta.rosetta.protocols.toolbox.sample_around module pyrosetta.rosetta.protocols.topology_broker module pyrosetta.rosetta.protocols.topology_broker.claims module pyrosetta.rosetta.protocols.topology_broker.weights module pyrosetta.rosetta.protocols.trajectory module pyrosetta.rosetta.protocols.trRosetta module pyrosetta.rosetta.protocols.trRosetta_protocols module pyrosetta.rosetta.protocols.trRosetta_protocols.constraint_generators module pyrosetta.rosetta.protocols.trRosetta_protocols.movers module pyrosetta.rosetta.protocols.ub_e2c module pyrosetta.rosetta.protocols.unfolded_state_energy_calculator module pyrosetta.rosetta.protocols.vardist_solaccess module pyrosetta.rosetta.protocols.viewer module pyrosetta.rosetta.protocols.viewer.graphics_states_param module pyrosetta.rosetta.protocols.vip module pyrosetta.rosetta.protocols.wum module pyrosetta.rosetta.RDGeom module pyrosetta.rosetta.RDKit module pyrosetta.rosetta.std module pyrosetta.rosetta.utility module pyrosetta.rosetta.utility.CSI module pyrosetta.rosetta.utility.excn module pyrosetta.rosetta.utility.factory module pyrosetta.rosetta.utility.file module pyrosetta.rosetta.utility.graph module pyrosetta.rosetta.utility.io module pyrosetta.rosetta.utility.io.mpi_stream module pyrosetta.rosetta.utility.json_spirit module pyrosetta.rosetta.utility.json_spirit.internal_ module pyrosetta.rosetta.utility.keys module pyrosetta.rosetta.utility.libsvm module pyrosetta.rosetta.utility.options module pyrosetta.rosetta.utility.pointer module pyrosetta.rosetta.utility.py module pyrosetta.rosetta.utility.signals module pyrosetta.rosetta.utility.sql_database module pyrosetta.rosetta.utility.tag module pyrosetta.rosetta.utility.thread module pyrosetta.rosetta.utility.tools module pyrosetta.rosetta.utility.type_traits module pyrosetta.rosetta.utility.type_traits.has_insertion_operator_implementation module pyrosetta.rosetta.utility.xsd_util module pyrosetta.rosetta.utility_exit_detail module pyrosetta.teaching module pyrosetta.tests module pyrosetta.tests.bindings module pyrosetta.tests.bindings.core module pyrosetta.tests.bindings.core.test_pose module pyrosetta.tests.distributed module pyrosetta.tests.distributed.cluster module pyrosetta.tests.distributed.test_dask_worker module pyrosetta.tests.numeric module pyrosetta.tests.protocols module pyrosetta.tests.protocols.indexed_structure_store module pyrosetta.toolbox module pyrosetta.toolbox.atom_pair_energy module pyrosetta.toolbox.cleaning module pyrosetta.toolbox.extract_coords_pose module pyrosetta.toolbox.generate_resfile module pyrosetta.toolbox.mutants module pyrosetta.toolbox.numpy_utils module pyrosetta.toolbox.py_jobdistributor module pyrosetta.toolbox.rcsb module pyrosetta.utility module PyRosettaEnergy_first (pyrosetta.rosetta.core.scoring.ScoreType attribute) PyRosettaEnergy_last (pyrosetta.rosetta.core.scoring.ScoreType attribute) PyRosettaException PyRosettaTwoBodyContextDependentEnergy_first (pyrosetta.rosetta.core.scoring.ScoreType attribute) PyRosettaTwoBodyContextDependentEnergy_last (pyrosetta.rosetta.core.scoring.ScoreType attribute) PyRosettaTwoBodyContextIndepenedentEnergy_first (pyrosetta.rosetta.core.scoring.ScoreType attribute) PyRosettaTwoBodyContextIndepenedentEnergy_last (pyrosetta.rosetta.core.scoring.ScoreType attribute) PyRotamerEliminator (class in pyrosetta.rosetta.core.pack.rotamer_set) PyRotamerEliminatorTaskOperation (class in pyrosetta.rosetta.core.pack.rotamer_set) python (pyrosetta.rosetta.core.scoring.ScoreType attribute) PythonLoggingSink (class in pyrosetta.logging_support) PythonLoggingSink.sentry (class in pyrosetta.logging_support) PythonPyExitCallback (class in pyrosetta) PyTracer (class in pyrosetta.rosetta.basic) PyTracer.sentry (class in pyrosetta.rosetta.basic) Pz (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData attribute) (pyrosetta.rosetta.core.chemical.gasteiger.GasteigerAtomTypeData.AtomicOrbitalTypes attribute) pz() (pyrosetta.rosetta.numeric.HomogeneousTransform_Double method) (pyrosetta.rosetta.numeric.HomogeneousTransform_double_t method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method)