Index – F

F (pyrosetta.rosetta.core.chemical.element.Elements attribute) F() (in module pyrosetta.rosetta.ObjexxFCL.format) (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_1_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_2_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_3_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_4_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_5_t method) (pyrosetta.rosetta.numeric.interpolation.spline.PolycubicSpline_6_t method) (pyrosetta.rosetta.numeric.interpolation.spline.TricubicSpline method) f0() (pyrosetta.rosetta.core.scoring.electron_density.KromerMann method) (pyrosetta.rosetta.core.scoring.fiber_diffraction.KromerMann method) f00() (pyrosetta.rosetta.core.optimization.DerivCheckDataPoint method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) f1() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) F1() (pyrosetta.rosetta.core.optimization.DOF_Node method) f1() (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams method) f11() (pyrosetta.rosetta.core.optimization.DerivCheckDataPoint method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) f1_force() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) f1_pore() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f1ij() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) f1ij_ (pyrosetta.rosetta.core.scoring.CSA property) (pyrosetta.rosetta.core.scoring.DC property) f2() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) F2() (pyrosetta.rosetta.core.optimization.DOF_Node method) f2() (pyrosetta.rosetta.core.scoring.DerivVectorPair method) (pyrosetta.rosetta.protocols.membrane.scoring.MEnvAtomParams method) f22() (pyrosetta.rosetta.core.optimization.DerivCheckDataPoint method) (pyrosetta.rosetta.core.optimization.DOF_DataPoint method) f2_force() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) f2_pore() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f2c() (pyrosetta.rosetta.protocols.cryst.Spacegroup method) (pyrosetta.rosetta.protocols.cryst.WallpaperGroup method) f2ij() (pyrosetta.rosetta.core.scoring.CSA method) (pyrosetta.rosetta.core.scoring.DC method) f2ij_ (pyrosetta.rosetta.core.scoring.CSA property) (pyrosetta.rosetta.core.scoring.DC property) f3ij() (pyrosetta.rosetta.core.scoring.CSA method) f3ij_ (pyrosetta.rosetta.core.scoring.CSA property) F_aa1 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_aa2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) f_cavity() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_cavity_dx() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_cavity_dy() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_cavity_dz() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_cavity_gradient() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) F_coorderr (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_dssp1 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_dssp2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_faatr (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_faatr_or_hb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_faatr_or_hbbb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) f_franklin() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_franklin_gradient() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) F_hb_bb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_hb_bb_sc (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_hb_sc (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) f_hydration() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_hydration_deriv_dz() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_imm1() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_imm1_deriv() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) F_lig (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_max_seqsep (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_maxdist2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_mindist2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_no_hb_bb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_nodisulf (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_noloops (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_not_restype (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_not_restype_one (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_occupancy (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_oneloop (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_pdb (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_restype (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_restype1 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_restype2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_restype_one (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_score (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_seqsep (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_ss1 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_ss2 (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) f_thickness() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_thickness_deriv() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_transition() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_transition_deriv() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) f_transition_deriv_m() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) f_transition_f1() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) f_transition_f2() (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab method) (pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle method) (pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry method) F_type_BB_BB (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_type_BB_PH (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_type_BB_PO (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_type_PH_PO (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_type_SC_BB (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_type_SC_PH (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_type_SC_PO (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_type_SC_SC (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) F_uniformfrag (pyrosetta.rosetta.core.scoring.motif.RPM_FilterStats property) fa_and_cen_sizes_for_archives() (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.MRSJobQueenChecker static method) fa_atr (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_atr() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) fa_atr_bb() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) fa_atr_dummy (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_atr_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_atr_sc_bb() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) fa_atr_wtd_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) fa_attr (pyrosetta.rosetta.protocols.features.helixAssembly.FragmentPair property) fa_center() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_cust_pair_dist (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_custom_pair_dist_data (pyrosetta.rosetta.core.scoring.min_pair_data attribute) fa_depth() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_disulfide_energy (pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType attribute) fa_dslf_respair_data (pyrosetta.rosetta.core.scoring.min_pair_data attribute) fa_dun (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_dun_cutoff() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) fa_dun_cutoff_ (pyrosetta.rosetta.protocols.match.upstream.BuildSet property) fa_dun_dev (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_dun_dev() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) fa_dun_dev_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_dun_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_dun_rot (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_dun_rot() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) fa_dun_rot_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_dun_semi (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_dun_semi() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) fa_dun_semi_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_dun_tot() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace method) fa_elec (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_aro_all (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_aro_aro (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_bb_bb (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_bb_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_base_base (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_base_base_fast (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_phos_base (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_phos_base_fast (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_phos_phos (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_phos_phos_fast (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_phos_sugr (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_phos_sugr_fast (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_sugr_base (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_sugr_base_fast (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_sugr_sugr (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_rna_sugr_sugr_fast (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_sc_sc (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_elec_wtd_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) FA_ElecEnergy (class in pyrosetta.rosetta.core.scoring.elec) FA_ElecEnergyAroAll (class in pyrosetta.rosetta.core.energy_methods) FA_ElecEnergyAroAllCreator (class in pyrosetta.rosetta.core.energy_methods) FA_ElecEnergyAroAro (class in pyrosetta.rosetta.core.energy_methods) FA_ElecEnergyAroAroCreator (class in pyrosetta.rosetta.core.energy_methods) FA_ElecEnergyCreator (class in pyrosetta.rosetta.core.scoring.elec) fa_fraction (pyrosetta.rosetta.protocols.features.helixAssembly.FragmentPair property) fa_grpelec (pyrosetta.rosetta.core.scoring.ScoreType attribute) FA_GrpElecEnergy (class in pyrosetta.rosetta.core.energy_methods) FA_GrpElecEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) fa_hatr (pyrosetta.rosetta.core.scoring.etable.EtableOptions property) fa_hatr() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) fa_intra_atr (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_atr_nonprotein (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_atr_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_atr_xover4 (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_elec (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_rep (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_rep_nonprotein (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_rep_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_rep_xover4 (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_RNA_base_phos_atr (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_RNA_base_phos_rep (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_RNA_base_phos_sol (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_sol (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_sol_nonprotein (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_sol_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_intra_sol_xover4 (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_is_independent() (pyrosetta.rosetta.core.conformation.symmetry.SymmetryInfo method) fa_mbenv (pyrosetta.rosetta.core.scoring.ScoreType attribute) Fa_MbenvEnergy (class in pyrosetta.rosetta.core.energy_methods) Fa_MbenvEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) fa_mbsolv (pyrosetta.rosetta.core.scoring.ScoreType attribute) Fa_MbsolvEnergy (class in pyrosetta.rosetta.core.energy_methods) Fa_MbsolvEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) Fa_Membed_update() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_pair (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_pair_aro_aro (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_pair_aro_pol (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_pair_pol_pol (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_penalty() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_proj() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_proj_coord() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_proj_deriv() (pyrosetta.rosetta.core.scoring.Membrane_FAEmbed method) fa_rep (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_rep_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) fa_rep_dummy (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_rep_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) FA_REP_SCORE (pyrosetta.rosetta.core.conformation.symmetry.SlideCriteriaType attribute) fa_sasa (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_scorefxn() (pyrosetta.rosetta.protocols.relax.loop.LoopRelaxMover method) fa_sol (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_sol_dummy (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_sol_ref (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_sol_wtd_ (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy property) fa_stack (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_stack_aro (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_stack_base_all() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) fa_stack_ext (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_stack_lower (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_stack_lr (pyrosetta.rosetta.core.scoring.ScoreType attribute) FA_STACK_NBLIST (pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum attribute) fa_stack_pair_nblist (pyrosetta.rosetta.core.scoring.min_pair_data attribute) fa_stack_rna_protein (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_stack_rna_protein_aro (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_stack_sol (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_stack_upper (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_vdw_tinker (pyrosetta.rosetta.core.scoring.ScoreType attribute) fa_water_to_bilayer (pyrosetta.rosetta.core.scoring.ScoreType attribute) FabConstraint (class in pyrosetta.rosetta.core.scoring.constraints) FabConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) factor() (pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent method) factorA() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) factorB() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) (pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover method) (pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover method) factorC() (pyrosetta.rosetta.protocols.simple_moves.BBConRotMover method) factors() (pyrosetta.rosetta.numeric.fourier.kiss_fft_state method) factorsLTE19() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) factorsLTE5() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) factory() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) factory_clear() (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) factory_name() (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t method) factory_register() (pyrosetta.rosetta.basic.datacache.WriteableCacheableDataFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLoaderFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceLocatorFactory method) (pyrosetta.rosetta.basic.resource_manager.ResourceManagerFactory method) (pyrosetta.rosetta.core.chemical.PatchOperationFactory method) (pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationFactory method) (pyrosetta.rosetta.core.io.silent.SilentStructFactory method) (pyrosetta.rosetta.core.pack.palette.PackerPaletteFactory method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibraryFactory method) (pyrosetta.rosetta.core.pack.task.operation.ResFilterFactory method) (pyrosetta.rosetta.core.pack.task.operation.ResLvlTaskOperationFactory method) (pyrosetta.rosetta.core.pack.task.operation.TaskOperationFactory method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintFactory method) (pyrosetta.rosetta.core.scoring.ScoringManager method) (pyrosetta.rosetta.core.select.jump_selector.JumpSelectorFactory method) (pyrosetta.rosetta.core.select.residue_selector.ResidueSelectorFactory method) (pyrosetta.rosetta.core.sequence.SequenceFactory method) (pyrosetta.rosetta.core.simple_metrics.SimpleMetricFactory method) (pyrosetta.rosetta.protocols.chemistries.ChemistryFactory method) (pyrosetta.rosetta.protocols.constraint_generator.ConstraintGeneratorFactory method) (pyrosetta.rosetta.protocols.evaluation.EvaluatorFactory method) (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory method) (pyrosetta.rosetta.protocols.filters.FilterFactory method) (pyrosetta.rosetta.protocols.genetic_algorithm.EntityElementFactory method) (pyrosetta.rosetta.protocols.jd2.JobInputterFactory method) (pyrosetta.rosetta.protocols.jd2.JobOutputterFactory method) (pyrosetta.rosetta.protocols.jd3.chunk_library_inputters.ChunkLibraryInputterFactory method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory method) (pyrosetta.rosetta.protocols.jd3.pose_inputters.PoseInputterFactory method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputterFactory method) (pyrosetta.rosetta.protocols.legacy_sewing.sampling.requirements.LegacyRequirementFactory method) (pyrosetta.rosetta.protocols.ligand_docking.rdf.RDFFunctionFactory method) (pyrosetta.rosetta.protocols.loops.loops_definers.LoopsDefinerFactory method) (pyrosetta.rosetta.protocols.moves.MoverFactory method) (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.cluster.ClusterMetricFactory method) (pyrosetta.rosetta.protocols.parser.DataLoaderFactory method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.GridFactory method) (pyrosetta.rosetta.protocols.rosetta_scripts.PosePropertyReporterFactory method) (pyrosetta.rosetta.protocols.rosetta_scripts.PoseSelectorFactory method) (pyrosetta.rosetta.protocols.sewing.requirements.AssemblyRequirementFactory method) (pyrosetta.rosetta.protocols.sewing.scoring.AssemblyScorerFactory method) (pyrosetta.rosetta.utility.factory.WidgetFactory_protocols_genetic_algorithm_EntityElementCreator_t method) facts_elec (pyrosetta.rosetta.core.scoring.ScoreType attribute) FACTS_GET_ALL_BORN_RADII (pyrosetta.rosetta.basic.ProfTag attribute) FACTS_POSE_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) FACTS_ROTAMER_BACKGROUND_ENERGIES (pyrosetta.rosetta.basic.ProfTag attribute) FACTS_ROTAMER_PAIR_ENERGIES (pyrosetta.rosetta.basic.ProfTag attribute) FACTS_ROTAMER_SET_INFO (pyrosetta.rosetta.core.conformation.RotamerSetCacheableDataType.Enum attribute) facts_sasa (pyrosetta.rosetta.core.scoring.ScoreType attribute) FACTS_SETUP_FOR_PACKING (pyrosetta.rosetta.basic.ProfTag attribute) facts_solv (pyrosetta.rosetta.core.scoring.ScoreType attribute) FACTSEnergy (class in pyrosetta.rosetta.core.energy_methods) FACTSEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FACTSPoseInfo (class in pyrosetta.rosetta.core.scoring.facts) FACTSPotential (class in pyrosetta.rosetta.core.scoring.facts) FACTSResidueInfo (class in pyrosetta.rosetta.core.scoring.facts) FACTSRotamerSetInfo (class in pyrosetta.rosetta.core.scoring.facts) FACTSRsdTypeInfo (class in pyrosetta.rosetta.core.scoring.facts) FACTSRsdTypeMap (class in pyrosetta.rosetta.core.scoring.facts) fadd (pyrosetta.rosetta.core.scoring.APBSConfig property) fade_energy() (in module pyrosetta.rosetta.core.scoring.hbonds) (pyrosetta.rosetta.core.scoring.hbonds.HBondOptions method) fade_zone() (pyrosetta.rosetta.core.scoring.func.FadeFunc method) FadeFunc (class in pyrosetta.rosetta.core.scoring.func) FadeInterval (class in pyrosetta.rosetta.core.scoring.hbonds) FaDockingSlideIntoContact (class in pyrosetta.rosetta.protocols.docking) FAELEC_CONTEXT_DATA (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) FAElecContextData (class in pyrosetta.rosetta.core.energy_methods) fafilter() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) (pyrosetta.rosetta.protocols.loophash.LoopHashMoverWrapper method) FAIL (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) fail() (pyrosetta.rosetta.utility.io.icstream method) (pyrosetta.rosetta.utility.io.irstream method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ocstream method) (pyrosetta.rosetta.utility.io.orstream method) (pyrosetta.rosetta.utility.io.ozstream method) (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) FAIL_BAD_INPUT (pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) FAIL_BAD_SETTINGS (pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus attribute) FAIL_DO_NOT_RETRY (pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) fail_on_missing_cache_ (pyrosetta.rosetta.core.simple_metrics.composite_metrics.BestMutationsFromProbabilitiesMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.CurrentProbabilityMetric property) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.ProbabilityConservationMetric property) (pyrosetta.rosetta.protocols.esm_perplexity.PseudoPerplexityMetric property) FAIL_RETRY (pyrosetta.rosetta.core.chemical.modifications.ChemistryStatus attribute) (pyrosetta.rosetta.protocols.moves.MoverStatus attribute) FAILED (pyrosetta.rosetta.protocols.monte_carlo.TrialResult attribute) failed_jobs() (pyrosetta.rosetta.protocols.jd3.JobTracker method) failIf() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) failIfAlmostEqual() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) failIfEqual() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) failUnless() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) failUnlessAlmostEqual() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) failUnlessEqual() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) failUnlessRaises() (pyrosetta.tests.bindings.core.test_pose.TestPoseIO method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor method) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent method) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs method) Failure (pyrosetta.rosetta.protocols.loops.loop_mover.LoopResult attribute) failureException (pyrosetta.tests.bindings.core.test_pose.TestPoseIO attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseResidueLabelAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPoseScoresAccessor attribute) (pyrosetta.tests.bindings.core.test_pose.TestPosesToSilent attribute) (pyrosetta.tests.distributed.test_dask_worker.TestDaskArgs attribute) fake_hit() (in module pyrosetta.rosetta.protocols.match) fake_working_moving_suite (pyrosetta.rosetta.protocols.stepwise.modeler.rna.InternalWorkingResidueParameter property) fallback() (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) fallback_strategy() (pyrosetta.rosetta.protocols.antibody.design.CDRSeqDesignOptions method) False (class in pyrosetta.rosetta.utility.type_traits.has_insertion_operator_implementation) (pyrosetta.rosetta.utility.tag.AutoBool attribute) false_behavior() (pyrosetta.rosetta.protocols.task_operations.StoreCompoundTaskMover method) false_movemap() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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) false_negative (pyrosetta.rosetta.numeric.RocStatus attribute) false_positive (pyrosetta.rosetta.numeric.RocStatus attribute) FalseFilter (class in pyrosetta.rosetta.protocols.filters) FalseFilterCreator (class in pyrosetta.rosetta.protocols.filters) FalseResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) FalseResidueSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) FaMPAsymEzCB (pyrosetta.rosetta.core.scoring.ScoreType attribute) FaMPAsymEzCBEnergy (class in pyrosetta.rosetta.core.energy_methods) FaMPAsymEzCBEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FaMPAsymEzCG (pyrosetta.rosetta.core.scoring.ScoreType attribute) FaMPAsymEzCGEnergy (class in pyrosetta.rosetta.core.energy_methods) FaMPAsymEzCGEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FaMPEnv (pyrosetta.rosetta.core.scoring.ScoreType attribute) FaMPEnvEnergy (class in pyrosetta.rosetta.core.energy_methods) FaMPEnvEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FaMPEnvSmooth (pyrosetta.rosetta.core.scoring.ScoreType attribute) FaMPEnvSmoothEnergy (class in pyrosetta.rosetta.core.energy_methods) FaMPEnvSmoothEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FaMPSolv (pyrosetta.rosetta.core.scoring.ScoreType attribute) FaMPSolvEnergy (class in pyrosetta.rosetta.core.energy_methods) FaMPSolvEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FARFAR_setup_using_user_input_VDW_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker method) FArray1_bool_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1_ObjexxFCL_FArray1D_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1_std_string_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1A_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1A_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1D_bool_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1D_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1D_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1D_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1D_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1D_ObjexxFCL_FArray1D_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1D_std_string_t (class in pyrosetta.rosetta.ObjexxFCL) FArray1D_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_bool_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_BBDepNRChiSample_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_BBDepScoreInterpData_1_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_BBDepScoreInterpData_2_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_BBDepScoreInterpData_3_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_BBDepScoreInterpData_4_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_BBDepScoreInterpData_5_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_BBIndNRChiSample_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_numeric_xyzVector_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_ObjexxFCL_FArray2D_float__star__t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_ObjexxFCL_ubyte_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_std_string_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_unsigned_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2A_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2A_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_bool_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_BBDepNRChiSample_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_BBDepScoreInterpData_1_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_BBDepScoreInterpData_2_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_BBDepScoreInterpData_3_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_BBDepScoreInterpData_4_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_BBDepScoreInterpData_5_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_BBIndNRChiSample_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_numeric_xyzVector_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_ObjexxFCL_FArray2D_float__star__t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_ObjexxFCL_ubyte_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_std_string_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_unsigned_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2D_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray2P_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_core_pack_dunbrack_BBDepScoreInterpData_1_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_core_pack_dunbrack_BBDepScoreInterpData_2_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_core_pack_dunbrack_BBDepScoreInterpData_3_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_core_pack_dunbrack_BBDepScoreInterpData_4_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_core_pack_dunbrack_BBDepScoreInterpData_5_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_std_complex_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_std_vector_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_unsigned_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3_utility_vector1_unsigned_int_std_allocator_unsigned_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3A_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_core_pack_dunbrack_BBDepScoreInterpData_1_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_core_pack_dunbrack_BBDepScoreInterpData_2_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_core_pack_dunbrack_BBDepScoreInterpData_3_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_core_pack_dunbrack_BBDepScoreInterpData_4_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_core_pack_dunbrack_BBDepScoreInterpData_5_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_std_complex_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_std_vector_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_unsigned_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3D_utility_vector1_unsigned_int_std_allocator_unsigned_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray3P_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray4_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray4_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray4_unsigned_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray4D_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray4D_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray4D_unsigned_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray5_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray5_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray5D_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray5D_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray5D_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_bool_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_BBDepNRChiSample_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_BBDepScoreInterpData_1_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_BBDepScoreInterpData_2_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_BBDepScoreInterpData_3_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_BBDepScoreInterpData_4_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_BBDepScoreInterpData_5_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_BBIndNRChiSample_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_int_t (class in pyrosetta.rosetta.ObjexxFCL) FARRAY_MANIPULATION (pyrosetta.rosetta.basic.ProfTag attribute) FArray_numeric_xyzVector_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_ObjexxFCL_FArray1D_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_ObjexxFCL_FArray2D_float__star__t (class in pyrosetta.rosetta.ObjexxFCL) FArray_ObjexxFCL_ubyte_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_std_complex_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_std_string_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_std_vector_unsigned_long_std_allocator_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) farray_to_array() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.DataBuffer method) FArray_unsigned_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_utility_vector1_double_std_allocator_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArray_utility_vector1_unsigned_int_std_allocator_unsigned_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_bool_ObjexxFCL_FArray1D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_bool_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_char_ObjexxFCL_FArray1D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepNRChiSample_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_1_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_2_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_3_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_4_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBDepScoreInterpData_5_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_BBIndNRChiSample_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_double_ObjexxFCL_FArray1D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_double_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_double_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_double_ObjexxFCL_FArray4D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_double_ObjexxFCL_FArray5D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_float_ObjexxFCL_FArray1D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_float_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_float_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_float_ObjexxFCL_FArray5D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_int_ObjexxFCL_FArray1D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_int_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_int_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_int_ObjexxFCL_FArray4D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_int_ObjexxFCL_FArray5D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_numeric_xyzVector_double_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_ObjexxFCL_FArray1D_int_ObjexxFCL_FArray1D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_ObjexxFCL_FArray2D_float__star__ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_ObjexxFCL_ubyte_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_std_complex_double_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_std_string_ObjexxFCL_FArray1D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_std_string_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_std_vector_unsigned_long_std_allocator_unsigned_long_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_unsigned_char_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_unsigned_char_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_unsigned_char_ObjexxFCL_FArray4D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_unsigned_long_ObjexxFCL_FArray1D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_unsigned_long_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_unsigned_long_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_utility_vector1_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_std_allocator_core_pack_dunbrack_cenrot_CentroidRotamerSampleData_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray2D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_utility_vector1_double_std_allocator_double_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayInitializer_utility_vector1_unsigned_int_std_allocator_unsigned_int_ObjexxFCL_FArray3D_t (class in pyrosetta.rosetta.ObjexxFCL) FArraySection_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArraySection_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArraySection_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArraySection_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_bool_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_char_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_BBDepNRChiSample_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_1_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_2_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_3_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_4_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_BBDepScoreInterpData_5_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_BBIndNRChiSample_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_double_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_float_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_int_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_std_string_t (class in pyrosetta.rosetta.ObjexxFCL) FArrayTraits_unsigned_long_t (class in pyrosetta.rosetta.ObjexxFCL) FAScatter (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) fascore() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure method) FASelectSlidingWindowLoopClosure (class in pyrosetta.rosetta.protocols.loops.loop_closure.ccd) fasol_cubic_poly1_close (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly1_close_flat (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly1_far (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly2_close (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly2_close_flat (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly2_far (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly_close (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly_close_end (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly_close_flat (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly_close_start (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly_far (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_cubic_poly_far_xhi() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) fasol_cubic_poly_far_xlo() (pyrosetta.rosetta.core.scoring.etable.Etable method) (pyrosetta.rosetta.core.scoring.etable.MembEtable method) fasol_final_weight (pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair property) fasol_max_dis2() (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) fast() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) (pyrosetta.rosetta.protocols.idealize.IdealizeMover method) fast_ccd_close_loops() (in module pyrosetta.rosetta.protocols.loops.loop_mover.perturb) fast_forward() (pyrosetta.rosetta.protocols.stepwise.legacy.screener.ProteinAtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.RNA_AtrRepScreener method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimpleRMSD_Screener 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_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.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.stepwise.screener.AlignRMSD_Screener method) (pyrosetta.rosetta.protocols.stepwise.screener.AnchorSugarScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseBinMapUpdater method) (pyrosetta.rosetta.protocols.stepwise.screener.BaseCentroidScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.BulgeApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.CentroidDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextResidueAlternative method) (pyrosetta.rosetta.protocols.stepwise.screener.FastForwardToNextRigidBody method) (pyrosetta.rosetta.protocols.stepwise.screener.IntegrationTestBreaker method) (pyrosetta.rosetta.protocols.stepwise.screener.O2PrimeScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PackScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PartitionContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PhosphateScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.PoseSelectionScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ProteinCCD_ClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.ResidueContactScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryResidueBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosableGeometryStubBasedScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.RNA_ChainClosureScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SampleApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.Scorer method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseResiduePairScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.StubApplier method) (pyrosetta.rosetta.protocols.stepwise.screener.StubDistanceScreener method) (pyrosetta.rosetta.protocols.stepwise.screener.SugarInstantiator method) (pyrosetta.rosetta.protocols.stepwise.screener.TagDefinition method) (pyrosetta.rosetta.protocols.stepwise.screener.VDW_BinScreener method) fast_forward_to_end() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSampler method) fast_forward_to_next_euler_gamma() (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) fast_forward_to_next_residue() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) FAST_FORWARD_TO_NEXT_RESIDUE_ALTERNATIVE (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) fast_forward_to_next_residue_pair() (in module pyrosetta.rosetta.protocols.stepwise.screener) (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) FAST_FORWARD_TO_NEXT_RIGID_BODY (pyrosetta.rosetta.protocols.stepwise.screener.StepWiseScreenerType attribute) fast_forward_to_next_rigid_body() (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueAlternatives method) (pyrosetta.rosetta.protocols.stepwise.sampler.rigid_body.RigidBodyStepWiseSamplerWithResidueList method) fast_forward_to_next_translation() (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) fast_full_atom_VDW_repulsion_screen (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) fast_restyping() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) fast_rmsd() (in module pyrosetta.rosetta.protocols.cluster.calibur) fast_scan() (pyrosetta.rosetta.protocols.rna.movers.RNA_LoopCloser method) fasta_file() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) fasta_file_contents() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) FastDensEnergy (class in pyrosetta.rosetta.core.energy_methods) FastDensEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FastDesign (class in pyrosetta.rosetta.protocols.denovo_design.movers) FastDesignCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) FASTER_IG_Repacker (class in pyrosetta.rosetta.protocols.pack_daemon) FASTERAnnealer (class in pyrosetta.rosetta.core.pack.annealer) FASTEREdge (class in pyrosetta.rosetta.core.pack.interaction_graph) FASTERInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) FASTERNode (class in pyrosetta.rosetta.core.pack.interaction_graph) FastForwardToNextResidueAlternative (class in pyrosetta.rosetta.protocols.stepwise.screener) FastForwardToNextRigidBody (class in pyrosetta.rosetta.protocols.stepwise.screener) FastGapMover (class in pyrosetta.rosetta.protocols.loophash) FastLinearFunc (class in pyrosetta.rosetta.protocols.moves) FastRelax (class in pyrosetta.rosetta.protocols.relax) FastRelaxCreator (class in pyrosetta.rosetta.protocols.relax) fastsaxs (pyrosetta.rosetta.core.scoring.ScoreType attribute) FastSAXSEnergy (class in pyrosetta.rosetta.core.energy_methods) FastSAXSEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FaSymDockingSlideTogether (class in pyrosetta.rosetta.protocols.symmetry) Fatal (pyrosetta.rosetta.basic.MemTracer property) (pyrosetta.rosetta.basic.MemTracerImpl property) (pyrosetta.rosetta.basic.Tracer property) (pyrosetta.rosetta.basic.TracerImpl property) FavorNativeResidue (class in pyrosetta.rosetta.protocols.protein_interface_design) FavorNativeResiduePreCycle (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) FavorNativeResiduePreCycleCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) FavorNonNativeResidue (class in pyrosetta.rosetta.protocols.protein_interface_design) FavorNonNativeResiduePreCycle (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) FavorNonNativeResiduePreCycleCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) FavorSequenceProfile (class in pyrosetta.rosetta.protocols.simple_moves) FavorSequenceProfileCreator (class in pyrosetta.rosetta.protocols.simple_moves) FavorSymmetricSequence (class in pyrosetta.rosetta.protocols.simple_moves) FavorSymmetricSequenceCreator (class in pyrosetta.rosetta.protocols.simple_moves) FaWaterToBilayerEnergy (class in pyrosetta.rosetta.protocols.membrane.scoring) FaWaterToBilayerEnergyCreator (class in pyrosetta.rosetta.protocols.membrane.scoring) fc_bg_ (pyrosetta.rosetta.core.pack.interaction_graph.exposed_hydrophobic_data property) fcen10() (pyrosetta.rosetta.core.scoring.CenListInfo method) fcen12() (pyrosetta.rosetta.core.scoring.CenListInfo method) fcen6() (pyrosetta.rosetta.core.scoring.CenListInfo method) Fd_like (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) FdF() (pyrosetta.rosetta.numeric.interpolation.spline.BicubicSpline method) (pyrosetta.rosetta.numeric.interpolation.spline.CubicSpline method) Fe (pyrosetta.rosetta.core.chemical.element.Elements attribute) FE2_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) FE3_COORDINATION (pyrosetta.rosetta.core.chemical.VariantType attribute) feature_types_ (pyrosetta.rosetta.protocols.comparative_modeling.features.ResidueFeatureFactory property) features_reporter_dependencies() (pyrosetta.rosetta.protocols.antibody.AntibodyFeatures method) (pyrosetta.rosetta.protocols.antibody.clusters.CDRClusterFeatures method) (pyrosetta.rosetta.protocols.features.AtomAtomPairFeatures method) (pyrosetta.rosetta.protocols.features.AtomInResidueAtomInResiduePairFeatures method) (pyrosetta.rosetta.protocols.features.AtomTypesFeatures method) (pyrosetta.rosetta.protocols.features.BatchFeatures 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.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.ProtocolFeatures method) (pyrosetta.rosetta.protocols.features.RadiusOfGyrationFeatures 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.UnrecognizedAtomFeatures method) (pyrosetta.rosetta.protocols.features.WaterFeatures method) features_reporter_xml_schema_group_name() (pyrosetta.rosetta.protocols.features.FeaturesReporterFactory static method) FeaturesReporter (class in pyrosetta.rosetta.protocols.features) FeaturesReporterCreator (class in pyrosetta.rosetta.protocols.features) FeaturesReporterFactory (class in pyrosetta.rosetta.protocols.features) featurizer_state() (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) fetch() (pyrosetta.rosetta.cppdb.backend.result method) (pyrosetta.rosetta.cppdb.backend.statements_cache method) (pyrosetta.rosetta.cppdb.result method) fetch_and_organize_data() (pyrosetta.rosetta.core.scoring.epr_deer.DEERDataCache method) fetch_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) ff() (pyrosetta.rosetta.core.scoring.saxs.FormFactor method) fft3() (in module pyrosetta.rosetta.numeric.fourier) fft3_dynamic() (in module pyrosetta.rosetta.numeric.fourier) FIBER_DIFFRACTION (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) FIBER_DIFFRACTION_CEN_SCATTERING (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) FIBER_DIFFRACTION_FA_SCATTERING (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) FiberDiffraction (class in pyrosetta.rosetta.core.scoring.fiber_diffraction) fiberdiffraction (pyrosetta.rosetta.core.scoring.ScoreType attribute) fiberdiffractiondens (pyrosetta.rosetta.core.scoring.ScoreType attribute) FiberDiffractionEnergy (class in pyrosetta.rosetta.core.energy_methods) FiberDiffractionEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FiberDiffractionEnergyDens (class in pyrosetta.rosetta.core.energy_methods) FiberDiffractionEnergyDensCreator (class in pyrosetta.rosetta.core.energy_methods) FibrilModelingClaimer (class in pyrosetta.rosetta.protocols.topology_broker) Field (class in pyrosetta.rosetta.core.io.pdb) figure_out_all_possible_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) figure_out_base_pair_partner() (in module pyrosetta.rosetta.protocols.rna.denovo) figure_out_chain_numbers_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_chain_numbers_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_conventional_chains_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_conventional_segids_from_full_model_info() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_dock_domain_map() (in module pyrosetta.rosetta.core.import_pose) figure_out_dock_domain_map_from_full_model_info_const() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_dofs() (pyrosetta.rosetta.core.pose.copydofs.CopyDofs method) figure_out_fixed_domain_map() (in module pyrosetta.rosetta.core.import_pose) figure_out_motif_mode() (in module pyrosetta.rosetta.core.import_pose) figure_out_moving_chain_break_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_chain_breaks() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_cutpoints_closed() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_cutpoints_closed_from_moving_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_partition_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) figure_out_moving_partition_res_for_jump() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_partition_res_for_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_moving_rna_chain_breaks() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) figure_out_neighbors() (pyrosetta.rosetta.protocols.stepwise.modeler.packer.StepWisePacker method) figure_out_pose_domain_map() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_pose_domain_map_const() (in module pyrosetta.rosetta.core.pose.full_model_info) figure_out_protein_modeling_info() (in module pyrosetta.rosetta.protocols.stepwise.modeler.protein) figure_out_reasonable_rna_fold_tree() (in module pyrosetta.rosetta.core.pose.rna) figure_out_rebuild_bulge_mode() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) figure_out_reference_res_for_jump() (in module pyrosetta.rosetta.protocols.toolbox.rigid_body) figure_out_reference_res_for_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_repackable_residues() (in module pyrosetta.rosetta.core.pack) figure_out_residue_numbers_from_line() (in module pyrosetta.rosetta.core.io.silent) (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) figure_out_root_and_moving_partition_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_root_partition_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) figure_out_sample_both_sugar_base_rotamer() (in module pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters) figure_out_sample_res() (in module pyrosetta.rosetta.core.import_pose) figure_out_secstruct() (in module pyrosetta.rosetta.core.pose.rna) figure_out_segment_ids_from_line() (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) figure_out_stepwise_movemap() (in module pyrosetta.rosetta.protocols.stepwise.modeler.movemap) figure_out_working_interface_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler.packer) figure_out_working_res() (in module pyrosetta.rosetta.core.import_pose) fij() (pyrosetta.rosetta.core.scoring.RDC method) fij_ (pyrosetta.rosetta.core.scoring.RDC property) file() (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.dna.PDBOutput method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Passport method) (pyrosetta.rosetta.protocols.environment.EXCN_Env_Security_Exception method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.forge.remodel.EXCN_RemoveCstsFailed method) (pyrosetta.rosetta.protocols.jd2.archive.EXCN_Archive method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JD2Failure method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter 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) file_basename() (in module pyrosetta.rosetta.utility) (in module pyrosetta.rosetta.utility.file) file_contents() (in module pyrosetta.rosetta.utility) file_delete() (in module pyrosetta.rosetta.utility.file) file_exists() (in module pyrosetta.rosetta.utility.file) (pyrosetta.rosetta.utility.Inline_File_Provider method) file_extension() (in module pyrosetta.rosetta.utility.file) file_full_path() (in module pyrosetta.rosetta.protocols.toolbox) file_inputs_for_job() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) file_is_atom_tree_diff() (in module pyrosetta.rosetta.core.import_pose.atom_tree_diffs) file_name() (pyrosetta.rosetta.protocols.canonical_sampling.DbTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.MetricRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.SilentTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.TrajectoryRecorder method) file_names() (pyrosetta.rosetta.protocols.simple_filters.FileRemoveFilter method) FILE_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) file_read() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzdesLoopsFile method) file_reading_token() (pyrosetta.rosetta.protocols.loops.Loops method) file_size() (in module pyrosetta.rosetta.utility.file) file_status() (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) FILE_VECTOR_OPTION (pyrosetta.rosetta.utility.options.OptionTypes attribute) filebuf (class in pyrosetta.rosetta.std) FileBuffer (class in pyrosetta.rosetta.protocols.checkpoint) FileConstraintGenerator (class in pyrosetta.rosetta.protocols.denovo_design.constraints) FileConstraintGeneratorCreator (class in pyrosetta.rosetta.protocols.denovo_design.constraints) FileContentsMap (class in pyrosetta.rosetta.utility.io) FileExistFilter (class in pyrosetta.rosetta.protocols.simple_filters) FileExistFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) FileJobOutputter (class in pyrosetta.rosetta.protocols.jd2) FileListResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileListResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileName (class in pyrosetta.rosetta.utility.file) filename (pyrosetta.rosetta.protocols.protein_interface_design.movers.VLBInstruction property) filename() (in module pyrosetta.rosetta.utility) (pyrosetta.rosetta.core.io.raw_data.DisulfideFile method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.io.StructFileRep method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfile method) (pyrosetta.rosetta.core.pack.task.operation.ReadResfileAndObeyLengthEvents method) (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Base method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_Sparky method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xeasy method) (pyrosetta.rosetta.protocols.noesy_assign.PeakFileFormat_xpk method) (pyrosetta.rosetta.protocols.quantum_annealing.InteractionGraphSummaryMetric method) (pyrosetta.rosetta.protocols.simple_filters.FileExistFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_moves.LoadPDBMover method) (pyrosetta.rosetta.utility.io.izstream method) (pyrosetta.rosetta.utility.io.ozstream method) filename2PDB (pyrosetta.rosetta.protocols.cluster.calibur.PreloadedPDB property) filename_for_job() (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) filename_for_output_job() (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter method) filenames() (pyrosetta.rosetta.core.import_pose.pose_stream.LazySilentFilePoseInputStream method) (pyrosetta.rosetta.core.import_pose.pose_stream.SilentFilePoseInputStream method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) filenames_ (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter property) FileNotFound (class in pyrosetta.rosetta.utility.excn) FileOption (class in pyrosetta.rosetta.utility.options) FileOptionKey (class in pyrosetta.rosetta.utility.options) FileRemoveFilter (class in pyrosetta.rosetta.protocols.simple_filters) FileRemoveFilterCreator (class in pyrosetta.rosetta.protocols.simple_filters) FileStream (class in pyrosetta.rosetta.basic.resource_manager.locator) FileSystemJobDistributor (class in pyrosetta.rosetta.protocols.jd2) FileSystemResourceLocator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileSystemResourceLocatorCreator (class in pyrosetta.rosetta.basic.resource_manager.locator) FileType (class in pyrosetta.rosetta.core.import_pose) filetype() (in module pyrosetta.rosetta.protocols.cluster.calibur) FileVectorOption (class in pyrosetta.rosetta.utility.options) FileVectorOptionKey (class in pyrosetta.rosetta.utility.options) fill() (pyrosetta.rosetta.basic.resource_manager.locator.StringResourceStream method) (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) fill_A_line() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs1) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs2) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs3) (in module pyrosetta.rosetta.protocols.scoring.methods.pcsTs4) fill_A_line_fast() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs2) fill_A_line_slow() (in module pyrosetta.rosetta.protocols.scoring.methods.pcs2) fill_author_records() (pyrosetta.rosetta.core.io.HeaderInformation method) fill_by_crossover() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) fill_by_mutation() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) fill_CA_coords() (in module pyrosetta.rosetta.protocols.toolbox) fill_compound_records() (pyrosetta.rosetta.core.io.HeaderInformation method) fill_contacts() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) fill_contacts_all_atom2() (pyrosetta.rosetta.protocols.contact_map.ContactMap method) fill_data() (in module pyrosetta.rosetta.protocols.recces) (pyrosetta.rosetta.core.scoring.sasa.SasaCalc method) fill_data_from_features() (pyrosetta.rosetta.core.io.rna.RDAT method) fill_designable_set() (pyrosetta.rosetta.protocols.pose_metric_calculators.SequenceComparison method) fill_downstream_children_res_and_tips() (in module pyrosetta.rosetta.core.conformation.carbohydrates) (in module pyrosetta.rosetta.core.pose.carbohydrates) fill_energy_map() (pyrosetta.rosetta.core.scoring.EnergyEdge method) fill_espGrid_values() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) fill_espGrid_values_with_type() (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) fill_experimental_technique_records() (pyrosetta.rosetta.core.io.HeaderInformation method) fill_f1_f2() (pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraint method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraint method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapMathConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionConstraint method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AmbiguousNMRDistanceConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.AtomToAxisConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BackboneStubLinearConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BasePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ConstantConstraint method) (pyrosetta.rosetta.core.scoring.constraints.Constraint method) (pyrosetta.rosetta.core.scoring.constraints.CoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DihedralPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.DistancePairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.FabConstraint method) (pyrosetta.rosetta.core.scoring.constraints.KofNConstraint method) (pyrosetta.rosetta.core.scoring.constraints.LocalCoordinateConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MembraneSpanTermZConstraint method) (pyrosetta.rosetta.core.scoring.constraints.MultiConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAtomPairConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedDihedralConstraint method) (pyrosetta.rosetta.core.scoring.constraints.NonResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueCouplingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeConstraint method) (pyrosetta.rosetta.core.scoring.constraints.ResidueTypeLinkingConstraint method) (pyrosetta.rosetta.core.scoring.constraints.RTConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SequenceProfileConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraint method) (pyrosetta.rosetta.core.scoring.constraints.SiteConstraintResidues method) (pyrosetta.rosetta.core.scoring.mhc_epitope_energy.MHCEpitopeConstraint method) (pyrosetta.rosetta.core.scoring.netcharge_energy.NetChargeConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.AmbiguousMultiConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.BindingSiteConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.COMCoordinateConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCoupling1BDConstraint method) (pyrosetta.rosetta.protocols.constraints_additional.SequenceCouplingConstraint method) (pyrosetta.rosetta.protocols.pockets.PocketConstraint method) fill_from_spanfile() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) fill_from_string() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_string_cs() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_string_residue_depth_version1() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_string_version1() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) fill_from_structure() (pyrosetta.rosetta.core.conformation.membrane.SpanningTopology method) fill_grid_with_backbone_heavyatom_spheres() (in module pyrosetta.rosetta.protocols.match) fill_grid_with_residue_heavyatom_spheres() (in module pyrosetta.rosetta.protocols.match) fill_grid_with_residue_spheres() (in module pyrosetta.rosetta.protocols.match) fill_h2o_hbond_set() (pyrosetta.rosetta.core.scoring.WaterAdductHBondPotential method) fill_hbond_bb_pair_score_dssp() (in module pyrosetta.rosetta.core.scoring.dssp) fill_hbond_set() (in module pyrosetta.rosetta.core.scoring.hbonds) fill_hbond_set_by_AHdist_threshold() (in module pyrosetta.rosetta.core.scoring.hbonds) fill_header_information() (pyrosetta.rosetta.core.io.rna.RDAT method) fill_header_record() (pyrosetta.rosetta.core.io.HeaderInformation method) fill_ideal_xyz_from_icoor() (pyrosetta.rosetta.core.chemical.MutableResidueType method) fill_in_default_jump_atoms() (in module pyrosetta.rosetta.core.pose.rna) fill_in_gaps() (in module pyrosetta.rosetta.protocols.frags) fill_intra_res_hbond_set() (in module pyrosetta.rosetta.core.scoring.hbonds) fill_jobs() (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) fill_keyword_records() (pyrosetta.rosetta.core.io.HeaderInformation method) fill_missing_atoms() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.Residue method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) fill_mutations_list() (pyrosetta.rosetta.protocols.pmut_scan.AlterSpecDisruptionDriver method) (pyrosetta.rosetta.protocols.pmut_scan.PointMutScanDriver method) fill_neighbor_residues() (in module pyrosetta.rosetta.core.select) fill_non_loop_cst_set() (in module pyrosetta.rosetta.protocols.forge.methods) fill_num_neighbors() (pyrosetta.rosetta.protocols.pose_metric_calculators.SequenceComparison method) fill_occlusions_1way() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) fill_other_struct_list() (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) fill_pairs() (pyrosetta.rosetta.core.pose.xyzStripeHashPose method) (pyrosetta.rosetta.numeric.geometry.hashing.xyzStripeHash method) fill_pose() (pyrosetta.rosetta.core.import_pose.PDBSilentStruct method) (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) (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.protocols.loop_grower.LoopComparator method) fill_pose_with_motif() (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) fill_records() (pyrosetta.rosetta.core.io.HeaderInformation method) fill_rna_data_info() (pyrosetta.rosetta.core.io.rna.RNA_DataReader method) fill_rotamer_matrix_from_db_file() (pyrosetta.rosetta.protocols.splice.RotLibdb method) (pyrosetta.rosetta.protocols.splice.SampleRotamersFromPDB_RotamerSetOperation method) fill_rotamer_vector() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (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) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) fill_solution() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.RNA_AnalyticLoopCloser method) fill_static_occlusions() (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) fill_struct() (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) fill_struct_with_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) fill_struct_with_submotif_info_list() (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) fill_template_frames_from_pdb() (in module pyrosetta.rosetta.core.fragment) fill_tenA_neighbor_residues() (in module pyrosetta.rosetta.core.select) fill_title_records() (pyrosetta.rosetta.core.io.HeaderInformation method) fill_top_level() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) fill_vdw_cached_rep_screen_info_from_command_line() (in module pyrosetta.rosetta.protocols.scoring) fill_vdw_cached_rep_screen_info_from_options() (in module pyrosetta.rosetta.protocols.scoring) fill_with() (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) fill_with_perturbations_of_existing_entities() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) fill_with_random_entities() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) fill_with_value() (pyrosetta.rosetta.protocols.qsar.qsarMap 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.HbaGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.HbdGrid method) (pyrosetta.rosetta.protocols.qsar.scoring_grid.LipidMemGrid 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.VdwGrid method) fillarray() (pyrosetta.rosetta.protocols.sic_dock.XfoxmScore method) FillAUTOTaskOperation (class in pyrosetta.rosetta.core.pack.task.operation) FillAUTOTaskOperationCreator (class in pyrosetta.rosetta.core.pack.task.operation) fillTargetPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) Filter (class in pyrosetta.rosetta.protocols.filters) (class in pyrosetta.rosetta.protocols.pose_selectors) (pyrosetta.rosetta.basic.citation_manager.CitedModuleType attribute) filter (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.mover_or_filter property) (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol.ParsedProtocolStep property) filter() (pyrosetta.rosetta.core.pack.task.operation.OperateOnCertainResidues method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotif method) (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.calc_taskop_filters.Sigmoid method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) (pyrosetta.rosetta.protocols.hotspot_hashing.HotspotStubSet method) (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) (pyrosetta.rosetta.protocols.monte_carlo.ResetBaselineMover method) (pyrosetta.rosetta.protocols.moves.IteratedConvergenceMover method) (pyrosetta.rosetta.protocols.protein_interface_design.filters.FilterScanFilter method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetTemperatureFactor method) (pyrosetta.rosetta.protocols.simple_ddg.ddG method) (pyrosetta.rosetta.protocols.simple_ddg.DdgFilter method) (pyrosetta.rosetta.protocols.simple_filters.DeltaFilter method) (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) (pyrosetta.rosetta.protocols.simple_moves.ContingentAcceptMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CombineLongLoopFilterer method) filter_acceptor_ligands() (in module pyrosetta.rosetta.protocols.magnesium) filter_behaviour() (pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter method) filter_by_constraints_energy_asymmetric() (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) filter_by_constraints_energy_symmetric() (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) filter_by_lj() (pyrosetta.rosetta.protocols.match.output.MatchCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) filter_by_sidechain_distance_asymmetric() (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) filter_by_sidechain_distance_symmetric() (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) filter_chain_closure() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) filter_chain_closure_distance() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) filter_chain_closure_halfway() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) filter_chunks() (pyrosetta.rosetta.protocols.pose_creation.SliceToMiniProteinMover method) filter_complex_cycles() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) filter_creator_map() (pyrosetta.rosetta.protocols.filters.FilterFactory method) filter_deltas() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) filter_exists() (pyrosetta.rosetta.protocols.filters.FilterFactory method) filter_for_moving_res_contact (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count property) filter_for_previous_clash (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count property) filter_for_previous_contact (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Filterer_Count property) filter_loop_neighbors_by_distance() (in module pyrosetta.rosetta.protocols.loops) filter_lores_base_pairs() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) filter_lores_base_pairs_early() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) filter_max_angle() (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) filter_max_bend() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_max_dist() (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_max_orthoangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_max_planeangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_max_twist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_min_angle() (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) filter_min_bend() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) filter_min_dist() (pyrosetta.rosetta.protocols.fldsgn.filters.HSSTripletFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_min_orthoangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_min_planeangle() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandHelixGeometryFilter method) filter_min_twist() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) FILTER_MODE (pyrosetta.rosetta.protocols.cluster.calibur.Clustering property) filter_motifs() (in module pyrosetta.rosetta.core.scoring.motif) filter_name() (pyrosetta.rosetta.protocols.calc_taskop_filters.RelativePoseFilter method) (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) (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.ConstraintClaimer method) filter_names() (pyrosetta.rosetta.protocols.match.MatcherTask method) filter_native_big_bins() (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) filter_neighbors_by_distance() (in module pyrosetta.rosetta.core.select) filter_non_aas() (pyrosetta.rosetta.protocols.task_operations.ThreadSequenceOperation method) filter_num() (pyrosetta.rosetta.protocols.denovo_design.movers.EXCN_FilterFailed method) filter_on() (pyrosetta.rosetta.protocols.flxbb.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge method) filter_out_high() (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousApolarSegmentFilter method) (pyrosetta.rosetta.protocols.simple_filters.LongestContinuousPolarSegmentFilter method) filter_out_low() (pyrosetta.rosetta.protocols.simple_filters.BuriedSurfaceAreaFilter method) filter_pareto_opt_poses() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) filter_redundant() (pyrosetta.rosetta.core.scoring.motif.MotifHits method) filter_scorefxn() (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) filter_seqpos_pareto_opt_ptmuts() (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) filter_similar() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) filter_spinlabel_ensemble_by_distance_check() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) filter_spinlabel_ensemble_by_mask() (pyrosetta.rosetta.core.scoring.nmr.NMRSpinlabel method) filter_spinlabel_ensemble_by_packerenergy() (in module pyrosetta.rosetta.protocols.nmr) filter_structs() (pyrosetta.rosetta.protocols.flxbb.DesignTask method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer method) (pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal method) filter_structurally_identical_motifs() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) filter_structurally_similar_motifs() (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) filter_tags (pyrosetta.rosetta.protocols.multistage_rosetta_scripts.ParsedTagCache property) filter_thresholds() (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) filter_type (class in pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter) filter_type() (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) filter_upstream_collisions_by_score() (pyrosetta.rosetta.protocols.match.MatcherTask method) filter_upstream_downstream_collisions() (pyrosetta.rosetta.protocols.match.MatcherTask method) filter_upstream_downstream_collisions_by_score() (pyrosetta.rosetta.protocols.match.MatcherTask method) filter_upstream_residue_collisions() (pyrosetta.rosetta.protocols.match.MatcherTask method) filter_val() (pyrosetta.rosetta.protocols.simple_filters.ReportFilter method) filter_value() (pyrosetta.rosetta.protocols.fldsgn.filters.CoreDunbrackFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.InterlockingAromaFilter method) (pyrosetta.rosetta.protocols.fldsgn.filters.ParallelBetaPairingPreferenceFilter method) filter_vdw() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) filter_weight() (pyrosetta.rosetta.protocols.topology_broker.ConstraintClaimer method) filter_xml_schema_group_name() (pyrosetta.rosetta.protocols.filters.FilterFactory static method) FilterByAmphetamine (class in pyrosetta.rosetta.protocols.constel) FilterByHistamine (class in pyrosetta.rosetta.protocols.constel) FilterByIndoleCOO (class in pyrosetta.rosetta.protocols.constel) FilterByProxTerm (class in pyrosetta.rosetta.protocols.constel) FilterBySASA (class in pyrosetta.rosetta.protocols.constel) FilterByTryptamine (class in pyrosetta.rosetta.protocols.constel) FilterCollection (class in pyrosetta.rosetta.protocols.filters) FilterCreator (class in pyrosetta.rosetta.protocols.filters) (class in pyrosetta.rosetta.protocols.pose_selectors) filtered_abego() (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) filtered_area() (pyrosetta.rosetta.protocols.simple_filters.ContactMolecularSurfaceFilter method) (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) filtered_base_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_pair_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_stack_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_stack_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_base_stagger_array() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) filtered_median_distance() (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) filtered_sc() (pyrosetta.rosetta.protocols.simple_filters.ShapeComplementarityFilter method) filtered_score() (pyrosetta.rosetta.protocols.simple_filters.PackStatFilter method) filtered_sheet_topology() (pyrosetta.rosetta.protocols.fldsgn.filters.SheetTopologyFilter method) filtered_ss() (pyrosetta.rosetta.protocols.fldsgn.filters.SecondaryStructureFilter method) filtered_type() (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) filtered_value() (pyrosetta.rosetta.protocols.fldsgn.filters.FragQualFilter method) (pyrosetta.rosetta.protocols.simple_filters.HolesFilter method) (pyrosetta.rosetta.protocols.simple_filters.InterRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.IntraRepeatContactFilter method) (pyrosetta.rosetta.protocols.simple_filters.SSElementMotifContactFilter method) FilteredSolutions (class in pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers) Filterer_Count (class in pyrosetta.rosetta.protocols.stepwise.modeler.rna) filterExemplars_ (pyrosetta.rosetta.protocols.pockets.CCluster property) FilterFactory (class in pyrosetta.rosetta.protocols.filters) FilterMover (class in pyrosetta.rosetta.protocols.moves) filterprevious() (pyrosetta.rosetta.protocols.loop_grower.LoopPartialSolutionStore method) FilterReportAsPoseExtraScoresMover (class in pyrosetta.rosetta.protocols.moves) FilterReportAsPoseExtraScoresMoverCreator (class in pyrosetta.rosetta.protocols.moves) FilterReporter (class in pyrosetta.rosetta.protocols.pose_reporters) FilterReporterCreator (class in pyrosetta.rosetta.protocols.pose_reporters) FilterReporterMover (class in pyrosetta.rosetta.protocols.moves) filters() (pyrosetta.rosetta.protocols.calc_taskop_filters.Operator method) (pyrosetta.rosetta.protocols.design_opt.GreedyOptMutationMover method) (pyrosetta.rosetta.protocols.design_opt.PointMutationCalculator method) (pyrosetta.rosetta.protocols.evolution.EvolutionaryDynamicsMover method) (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) (pyrosetta.rosetta.protocols.monte_carlo.GenericMonteCarloMover method) (pyrosetta.rosetta.protocols.monte_carlo.GenericSimulatedAnnealer method) FilterScanFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) FilterScanFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) FilterStructs (class in pyrosetta.rosetta.protocols.flxbb) FilterStructs_Packstat (class in pyrosetta.rosetta.protocols.flxbb) FilterStructs_TotalCharge (class in pyrosetta.rosetta.protocols.flxbb) FilterValueMetric (class in pyrosetta.rosetta.protocols.filters) FilterValueMetricCreator (class in pyrosetta.rosetta.protocols.filters)

final (pyrosetta.rosetta.protocols.jd2.archive.MPIArchiveJobDistributor.CompletionMessage property) final_check_sw_by_dis() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) final_cleanup() (pyrosetta.rosetta.protocols.protein_interface_design.movers.PlaceSimultaneouslyMover method) final_design_min() (in module pyrosetta.rosetta.protocols.ncbb) final_fold_tree() (pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC method) (pyrosetta.rosetta.protocols.abinitio.KinematicControl method) (pyrosetta.rosetta.protocols.topology_broker.TopologyBroker method) final_frlx_rounds() (pyrosetta.rosetta.protocols.cyclic_peptide.CrosslinkerMover method) final_iter() (pyrosetta.rosetta.protocols.mpi_refinement.Scheduler method) final_pose() (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) final_repack() (pyrosetta.rosetta.protocols.grafting.AnchoredGraftMover method) (pyrosetta.rosetta.protocols.grafting.CCDEndsGraftMover method) final_score() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) final_scorefxn() (pyrosetta.rosetta.protocols.rosetta_scripts.ParsedProtocol method) final_scores() (pyrosetta.rosetta.protocols.residue_optimization.MetapatchEnumeration method) final_test() (pyrosetta.rosetta.protocols.motifs.MotifHit method) FINALIZE (pyrosetta.rosetta.basic.ProfTag attribute) Finalize() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) finalize() (pyrosetta.rosetta.core.id.AtomID_Map_AtomID method) (pyrosetta.rosetta.core.id.AtomID_Map_bool method) (pyrosetta.rosetta.core.id.AtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_core_scoring_packstat_LR_MP_AtomData_t method) (pyrosetta.rosetta.core.id.AtomID_Map_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_numeric_xyzVector_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_Real method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.core.id.AtomID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.core.id.AtomID_Map_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_bool_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_core_id_TorsionID_t method) (pyrosetta.rosetta.core.id.DOF_ID_Map_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_bool_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_core_id_NamedAtomID_t method) (pyrosetta.rosetta.core.id.NamedAtomID_Map_NamedAtomID method) (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionData method) (pyrosetta.rosetta.core.scoring.CenRotEnvPairPotential method) (pyrosetta.rosetta.core.scoring.EnvPairPotential method) (pyrosetta.rosetta.core.scoring.membrane.MembraneData method) (pyrosetta.rosetta.core.scoring.Membrane_FAPotential method) (pyrosetta.rosetta.core.scoring.MembranePotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.SmoothEnvPairPotential method) (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.fldsgn.topology.DimerPairings method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies method) (pyrosetta.rosetta.protocols.rna.denovo.output.RNA_FragmentMonteCarloOutputter method) (pyrosetta.rosetta.protocols.scoring.InterchainPotential method) (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseRNA_PoseSelection method) (pyrosetta.rosetta.protocols.stepwise.legacy.screener.SimplePoseSelection method) (pyrosetta.rosetta.protocols.trajectory.DbTrajectoryWriter method) finalize_after_derivatives() (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) finalize_after_minimizing() (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) finalize_author_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_batch() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) finalize_claims() (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) finalize_compound_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_de_novo_scoretable_from_energies() (pyrosetta.rosetta.core.chemical.mainchain_potential.MainchainScoreTable method) finalize_experimental_technique_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_hbond_graph() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) finalize_keyword_records() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_parse() (pyrosetta.rosetta.core.io.HeaderInformation method) finalize_scoring() (pyrosetta.rosetta.protocols.noesy_assign.DistanceScoreMover method) finalize_simulation() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) (pyrosetta.rosetta.protocols.backrub.BackrubSidechainMover method) (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.BiasEnergy 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.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.PDBTrajectoryRecorder method) (pyrosetta.rosetta.protocols.canonical_sampling.ProgressBarObserver 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.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) finalize_stub_set() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) finalize_stub_sets() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) finalize_total_energy() (pyrosetta.rosetta.core.energy_methods.AACompositionEnergy method) (pyrosetta.rosetta.core.energy_methods.AARepeatEnergy method) (pyrosetta.rosetta.core.energy_methods.Abego method) (pyrosetta.rosetta.core.energy_methods.ArgCationPiEnergy method) (pyrosetta.rosetta.core.energy_methods.AromaticBackboneRestraintEnergy method) (pyrosetta.rosetta.core.energy_methods.AspartimidePenaltyEnergy method) (pyrosetta.rosetta.core.energy_methods.BranchEnergy method) (pyrosetta.rosetta.core.energy_methods.Burial_v2Energy method) (pyrosetta.rosetta.core.energy_methods.BurialEnergy method) (pyrosetta.rosetta.core.energy_methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.CCS_IMMSEnergy method) (pyrosetta.rosetta.core.energy_methods.CenHBEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifDegreeEnergy method) (pyrosetta.rosetta.core.energy_methods.CenPairMotifEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.CenRotPairEnergy method) (pyrosetta.rosetta.core.energy_methods.CentroidDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.ChemicalShiftAnisotropyEnergy method) (pyrosetta.rosetta.core.energy_methods.ContactOrderEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextDependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.ContextIndependentGeometricSolEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.CovalentLabelingFAEnergy method) (pyrosetta.rosetta.core.energy_methods.CustomAtomPairEnergy method) (pyrosetta.rosetta.core.energy_methods.D2H_SA_Energy method) (pyrosetta.rosetta.core.energy_methods.DEEREnergy method) (pyrosetta.rosetta.core.energy_methods.DEPC_MS_Energy method) (pyrosetta.rosetta.core.energy_methods.dfire.DFIRE_Energy method) (pyrosetta.rosetta.core.energy_methods.DipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.energy_methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.DisulfideMatchingEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_DihedralEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.energy_methods.DNA_ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.DNAChiEnergy method) (pyrosetta.rosetta.core.energy_methods.DNATorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.DumpTrajectoryEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAllAtomCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensAtomwiseEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensCenEnergy method) (pyrosetta.rosetta.core.energy_methods.ElecDensEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvEnergy method) (pyrosetta.rosetta.core.energy_methods.EnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.ExactOccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAll method) (pyrosetta.rosetta.core.energy_methods.FA_ElecEnergyAroAro method) (pyrosetta.rosetta.core.energy_methods.FA_GrpElecEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbenvEnergy method) (pyrosetta.rosetta.core.energy_methods.Fa_MbsolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FACTSEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCBEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPAsymEzCGEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.FaMPSolvEnergy method) (pyrosetta.rosetta.core.energy_methods.FastDensEnergy method) (pyrosetta.rosetta.core.energy_methods.FastSAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergy method) (pyrosetta.rosetta.core.energy_methods.FiberDiffractionEnergyDens method) (pyrosetta.rosetta.core.energy_methods.FreeDOF_Energy method) (pyrosetta.rosetta.core.energy_methods.FullatomDisulfideEnergy method) (pyrosetta.rosetta.core.energy_methods.GaussianOverlapEnergy method) (pyrosetta.rosetta.core.energy_methods.GenBornEnergy method) (pyrosetta.rosetta.core.energy_methods.GenericBondedEnergy method) (pyrosetta.rosetta.core.energy_methods.GoapEnergy method) (pyrosetta.rosetta.core.energy_methods.HackAroEnergy method) (pyrosetta.rosetta.core.energy_methods.HolesEnergy method) (pyrosetta.rosetta.core.energy_methods.HRF_MSLabelingEnergy method) (pyrosetta.rosetta.core.energy_methods.HRFDynamicsEnergy method) (pyrosetta.rosetta.core.energy_methods.HybridVDW_Energy method) (pyrosetta.rosetta.core.energy_methods.HydroxylTorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.IntermolEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.energy_methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.energy_methods.LK_hack method) (pyrosetta.rosetta.core.energy_methods.LK_PolarNonPolarEnergy method) (pyrosetta.rosetta.core.energy_methods.LoopCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvPenalties method) (pyrosetta.rosetta.core.energy_methods.MembraneEnvSmoothEnergy method) (pyrosetta.rosetta.core.energy_methods.MembraneLipo method) (pyrosetta.rosetta.core.energy_methods.MgEnergy method) (pyrosetta.rosetta.core.energy_methods.MHCEpitopeEnergy method) (pyrosetta.rosetta.core.energy_methods.MissingEnergy method) (pyrosetta.rosetta.core.energy_methods.MotifDockEnergy method) (pyrosetta.rosetta.core.energy_methods.MPCbetaEnergy method) (pyrosetta.rosetta.core.energy_methods.MPEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.MPHelicalityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPPairEnergy method) (pyrosetta.rosetta.core.energy_methods.MPResidueLipophilicityEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.core.energy_methods.MPSpanInsertionEnergy method) (pyrosetta.rosetta.core.energy_methods.MultipoleElecEnergy method) (pyrosetta.rosetta.core.energy_methods.NetChargeEnergy method) (pyrosetta.rosetta.core.energy_methods.NPDHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy method) (pyrosetta.rosetta.core.energy_methods.OccludedHbondSolEnergy_onebody method) (pyrosetta.rosetta.core.energy_methods.OmegaTetherEnergy method) (pyrosetta.rosetta.core.energy_methods.OtherPoseEnergy method) (pyrosetta.rosetta.core.energy_methods.P_AA_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_pp_Energy method) (pyrosetta.rosetta.core.energy_methods.P_AA_ss_Energy method) (pyrosetta.rosetta.core.energy_methods.PackStatEnergy method) (pyrosetta.rosetta.core.energy_methods.PairEnergy method) (pyrosetta.rosetta.core.energy_methods.PeptideBondEnergy method) (pyrosetta.rosetta.core.energy_methods.pHEnergy method) (pyrosetta.rosetta.core.energy_methods.PointWaterEnergy method) (pyrosetta.rosetta.core.energy_methods.PoissonBoltzmannEnergy method) (pyrosetta.rosetta.core.energy_methods.ProClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.ProQ_Energy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy method) (pyrosetta.rosetta.core.energy_methods.RamachandranEnergy2B method) (pyrosetta.rosetta.core.energy_methods.RamaPreProEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergy method) (pyrosetta.rosetta.core.energy_methods.ReferenceEnergyNoncanonical method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy method) (pyrosetta.rosetta.core.energy_methods.ResidualDipolarCouplingEnergy_Rohl method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_Fast method) (pyrosetta.rosetta.core.energy_methods.RG_Energy_RNA method) (pyrosetta.rosetta.core.energy_methods.RG_LocalEnergy method) (pyrosetta.rosetta.core.energy_methods.RingClosureEnergy method) (pyrosetta.rosetta.core.energy_methods.RMS_Energy method) (pyrosetta.rosetta.core.energy_methods.RNA_BulgeEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalMappingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_CoarseDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_DataBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FA_ElecEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomStackingEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_FullAtomVDW_BasePhosphate method) (pyrosetta.rosetta.core.energy_methods.RNA_JR_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_LJ_BaseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_MgPointEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PairwiseLowResolutionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_PartitionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_StubCoordinateEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SugarCloseEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_TorsionEnergy method) (pyrosetta.rosetta.core.energy_methods.RNA_VDW_Energy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResPairDistEnergy method) (pyrosetta.rosetta.core.energy_methods.RNP_LowResStackEnergy method) (pyrosetta.rosetta.core.energy_methods.SA_Energy method) (pyrosetta.rosetta.core.energy_methods.SASAEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergy method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyCEN method) (pyrosetta.rosetta.core.energy_methods.SAXSEnergyFA method) (pyrosetta.rosetta.core.energy_methods.SecondaryStructureEnergy method) (pyrosetta.rosetta.core.energy_methods.SequenceDependentRefEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothCenPairEnergy method) (pyrosetta.rosetta.core.energy_methods.SmoothEnvEnergy method) (pyrosetta.rosetta.core.energy_methods.SplitUnfoldedTwoBodyEnergy method) (pyrosetta.rosetta.core.energy_methods.SSElementMotifContactEnergy method) (pyrosetta.rosetta.core.energy_methods.StackElecEnergy method) (pyrosetta.rosetta.core.energy_methods.SuckerEnergy method) (pyrosetta.rosetta.core.energy_methods.SugarBackboneEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfEnergy method) (pyrosetta.rosetta.core.energy_methods.SurfVolEnergy method) (pyrosetta.rosetta.core.energy_methods.SymmetricLigandEnergy method) (pyrosetta.rosetta.core.energy_methods.TNA_SuiteEnergy method) (pyrosetta.rosetta.core.energy_methods.UnfoldedStateEnergy method) (pyrosetta.rosetta.core.energy_methods.VdWTinkerEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductHBondEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterAdductIntraEnergy method) (pyrosetta.rosetta.core.energy_methods.WaterSpecificEnergy method) (pyrosetta.rosetta.core.energy_methods.XtalMLEnergy method) (pyrosetta.rosetta.core.energy_methods.YHHPlanarityEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.cenrot.CenRotDunEnergy method) (pyrosetta.rosetta.core.pack.dunbrack.DunbrackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.approximate_buried_unsat_penalty.ApproximateBuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.BuriedUnsatPenalty method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.hbnet_energy.HBNetEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.lk_dome.LK_DomePackEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintEnergy method) (pyrosetta.rosetta.core.pack.guidance_scoreterms.voids_penalty_energy.VoidsPenaltyEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.carbon_hbonds.CarbonHBondEnergy method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintsEnergy method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy method) (pyrosetta.rosetta.core.scoring.elec.FA_ElecEnergy method) (pyrosetta.rosetta.core.scoring.etable.AnalyticEtableEnergy method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_AnalyticEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.BaseEtableEnergy_core_scoring_etable_TableLookupEtableEnergy_t method) (pyrosetta.rosetta.core.scoring.etable.TableLookupEtableEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.HBondEnergy method) (pyrosetta.rosetta.core.scoring.interface_.DDPscore method) (pyrosetta.rosetta.core.scoring.lkball.LK_BallEnergy method) (pyrosetta.rosetta.core.scoring.lkball.LK_DomeEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextDependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentLRTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondAngleEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMBondLengthEnergy method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyInter method) (pyrosetta.rosetta.core.scoring.methods.MMLJEnergyIntra method) (pyrosetta.rosetta.core.scoring.methods.MMTorsionEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerPSSMEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerRefEnergy method) (pyrosetta.rosetta.core.scoring.methods.NMerSVMEnergy method) (pyrosetta.rosetta.core.scoring.methods.OneBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.TwoBodyEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.nv.NVscore method) (pyrosetta.rosetta.core.scoring.orbitals.OrbitalsScore method) (pyrosetta.rosetta.core.scoring.packing.HolesEnergyRes method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftPotential method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.sym_e.symEnergy method) (pyrosetta.rosetta.core.scoring.vdwaals.VDW_Energy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.membrane.scoring.FaWaterToBilayerEnergy method) (pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy method) (pyrosetta.rosetta.protocols.nmr.pre.PREEnergy method) (pyrosetta.rosetta.protocols.nmr.rdc.RDCEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.EnsembleEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainEnvEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.InterchainPairEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs.PCS_Energy method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs1.PCS_Energy_Ts1 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs3.PCS_Energy_Ts3 method) (pyrosetta.rosetta.protocols.scoring.methods.pcsTs4.PCS_Energy_Ts4 method) (pyrosetta.rosetta.protocols.scoring.methods.ResidualDipolarCouplingEnergyRigidSegments method) (pyrosetta.rosetta.protocols.scoring.methods.saxs.PDDFEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.SpecialRotamerEnergy method) (pyrosetta.rosetta.protocols.scoring.methods.TargetClashEnergy method) (pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy method) FinalizeAromatic() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) finalized() (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) finalized_energies() (pyrosetta.rosetta.core.scoring.Energies method) (pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies method) (pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies method) FinalizeUnhybridized() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom method) FinalMinimizer (class in pyrosetta.rosetta.protocols.ligand_docking) FinalMinimizerCreator (class in pyrosetta.rosetta.protocols.ligand_docking) FinalRMSDComparator (class in pyrosetta.rosetta.protocols.pose_length_moves) find() (pyrosetta.rosetta.core.pose.PDBPoseMap method) (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring 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.protein.ProteinMainChainStepWiseSampler method) find_another_representative_for_unlikely_rotamer() (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) find_antiparallel() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) find_assignments() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakList method) find_attach_pt() (in module pyrosetta.rosetta.protocols.ligand_docking) find_automatically() (pyrosetta.rosetta.protocols.protein_interface_design.movers.AddChainBreak method) find_basepairs() (in module pyrosetta.rosetta.core.scoring.dna) (in module pyrosetta.rosetta.protocols.dna) find_best_match() (in module pyrosetta.rosetta.core.chemical) find_bond_torsion_with_nearest_orientation() (in module pyrosetta.rosetta.core.conformation) find_bonds_in_rings() (in module pyrosetta.rosetta.core.chemical) find_bound_waters_that_are_daughters_in_fold_tree() (in module pyrosetta.rosetta.protocols.magnesium) find_by_atmpairno() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) find_by_bondno() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) find_cache_file() (in module pyrosetta.rosetta.basic.database) find_char_location_in_string() (pyrosetta.rosetta.protocols.evolution.AlignmentGapInserter method) find_chi_bonds() (in module pyrosetta.rosetta.core.chemical) find_chunk() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) find_clashing_shell() (in module pyrosetta.rosetta.core.pack.task.residue_selector) find_clashing_shells() (in module pyrosetta.rosetta.core.pack.task.residue_selector) find_closest() (in module pyrosetta.rosetta.core.membrane) (pyrosetta.rosetta.protocols.simple_moves.ExplicitWaterMover method) find_closest_atom() (in module pyrosetta.rosetta.protocols.metal_interface) find_closest_backbone() (pyrosetta.rosetta.protocols.motifs.IRCollection method) Find_Closest_Intersect_SQ() (in module pyrosetta.rosetta.protocols.pockets) find_closest_occupied_point() (pyrosetta.rosetta.protocols.loop_grower.DensSkeleton method) find_closest_pnts() (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) find_closest_to_average() (pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation method) find_column() (pyrosetta.rosetta.cppdb.result method) find_common_intersection_atoms() (in module pyrosetta.rosetta.core.scoring.power_diagram) find_connected_components() (in module pyrosetta.rosetta.utility.graph) find_connecting_jump() (in module pyrosetta.rosetta.protocols.forge.methods) find_constraints_to_ligand() (pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter method) (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) find_curr_hbonds_to_upper_neighbors() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) find_current_disulfides() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) find_cutpoint() (in module pyrosetta.rosetta.protocols.forge.methods) find_cutpoint_from_secondary_structure() (in module pyrosetta.rosetta.protocols.fold_from_loops.utils) find_cutpoint_variants() (in module pyrosetta.rosetta.core.scoring.methods) find_data() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) find_data_and_bin() (pyrosetta.rosetta.core.scoring.bin_transitions.BinTransitionCalculator method) find_database_path() (in module pyrosetta.rosetta.basic.database) find_dbase_entry() (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceIn method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceInTail method) find_design_interface() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) find_design_interface_arg_sweep() (pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface method) find_disulfide_postions() (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) find_disulfides_in_the_neighborhood() (pyrosetta.rosetta.protocols.forge.remodel.RemodelDesignMover method) find_disulfs_in_range() (in module pyrosetta.rosetta.protocols.splice) find_downstream_connection_res() (in module pyrosetta.rosetta.protocols.stepwise.modeler) find_edge() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph 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.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.NPDHBSimpleInteractionGraph 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.SimpleInteractionGraph 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.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintNode method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.EnergyNode method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph method) (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.MinimizationNode method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborNode method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborNode 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.jd3.JobDigraph method) (pyrosetta.rosetta.protocols.legacy_sewing.ModelNode 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) (pyrosetta.rosetta.utility.graph.LowMemNode method) (pyrosetta.rosetta.utility.graph.Node method) find_edge_from() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) find_edge_to() (pyrosetta.rosetta.protocols.jd3.JobDirectedNode method) (pyrosetta.rosetta.utility.graph.DirectedNode method) find_energy_edge() (pyrosetta.rosetta.core.scoring.EnergyGraph method) find_existing_residues() (in module pyrosetta.rosetta.protocols.evaluation) find_farthest() (in module pyrosetta.rosetta.core.membrane) find_filter_or_die() (in module pyrosetta.rosetta.protocols.moves) find_first_interface_residue() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) find_first_not_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_first_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_first_slice() (pyrosetta.rosetta.core.scoring.packstat.LeeRichards method) find_geometric_center_for_constrained_lig_atoms() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) find_global_pose_number() (pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver method) find_glycan_sequence_file() (in module pyrosetta.rosetta.core.chemical.carbohydrates) find_hash_edge() (pyrosetta.rosetta.protocols.legacy_sewing.SewGraph method) find_hb_paths() (in module pyrosetta.rosetta.core.scoring.hbonds) (pyrosetta.rosetta.core.simple_metrics.per_residue_metrics.WaterMediatedHbondMetric method) find_hbonds_in_residue_pair() (in module pyrosetta.rosetta.core.pack.hbonds) find_hbs_for_nbrs_alt_state_step1() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) find_hbs_for_nbrs_alt_state_step2() (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleNode method) find_helices_over_length() (in module pyrosetta.rosetta.protocols.aa_composition) find_helix_vector() (pyrosetta.rosetta.core.energy_methods.MPSpanAngleEnergy method) (pyrosetta.rosetta.protocols.simple_filters.HelixHelixAngleFilter method) find_hits() (pyrosetta.rosetta.protocols.match.Matcher method) find_in_pose_if_missing_from_header() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzCstTemplateRes method) find_index_for_loop_landing_at_domain() (pyrosetta.rosetta.core.scoring.loop_graph.LoopCycle method) find_index_in_other_pose_list() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) find_interface_jump() (in module pyrosetta.rosetta.protocols.ddg.CartesianddG) find_intersections() (in module pyrosetta.rosetta.core.scoring.power_diagram) find_job_edge() (pyrosetta.rosetta.protocols.jd3.JobDigraph method) find_jump_number_at_suite() (in module pyrosetta.rosetta.protocols.stepwise.modeler) find_jump_rec() (in module pyrosetta.rosetta.protocols.denovo_design) find_key_cl() (pyrosetta.rosetta.utility.options.OptionCollection method) find_key_file() (pyrosetta.rosetta.utility.options.OptionCollection static method) find_label() (pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver method) find_last() (pyrosetta.rosetta.ObjexxFCL.Cstring method) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_non_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_not_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_of() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_last_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_length() (pyrosetta.rosetta.protocols.task_operations.DatabaseThread method) find_ligands() (in module pyrosetta.rosetta.protocols.flxbb) find_local_pose_number() (pyrosetta.rosetta.protocols.topology_broker.SequenceNumberResolver method) find_lowest_constraint_energy_residue() (in module pyrosetta.rosetta.protocols.protein_interface_design) find_matching_res() (pyrosetta.rosetta.protocols.splice.RotLibOut method) find_max_frag() (pyrosetta.rosetta.protocols.hybridization.TMalign method) find_max_over() (pyrosetta.rosetta.core.chemical.VDDistanceMatrix method) find_max_r() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_metalbinding_atoms() (in module pyrosetta.rosetta.core.util) find_metalbinding_atoms_for_complex() (in module pyrosetta.rosetta.core.util) find_metalbinding_atoms_helper() (in module pyrosetta.rosetta.core.util) find_min_xyz() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_minimization_edge() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) find_mod_terminus() (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) find_motifs() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) find_motifs_with_radius() (pyrosetta.rosetta.core.scoring.motif.MotifHash method) find_mover_or_die() (in module pyrosetta.rosetta.protocols.moves) find_native() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) find_nbr_dist() (in module pyrosetta.rosetta.core.chemical) find_nearest_disulfide() (in module pyrosetta.rosetta.protocols.rosetta_scripts) find_nearest_res() (in module pyrosetta.rosetta.protocols.rosetta_scripts) find_nearest_residue() (in module pyrosetta.rosetta.protocols.protein_interface_design) find_nearest_residue_to_coord() (in module pyrosetta.rosetta.protocols.protein_interface_design.movers) find_neighbors() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) find_neighbors_restricted() (in module pyrosetta.rosetta.core.conformation) find_new_jump_residue() (pyrosetta.rosetta.protocols.simple_moves.asym_fold_and_dock.AsymFoldandDockMoveRbJumpMover method) find_new_symmetric_jump_residues() (in module pyrosetta.rosetta.core.pose.symmetry) find_next_vertex_with_smallest_dist() (in module pyrosetta.rosetta.core.scoring.power_diagram) find_non_protein_chunks() (in module pyrosetta.rosetta.protocols.loops) find_non_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_num_scattering_atoms() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_optimal_rotation() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) find_orientations_and_lengths() (in module pyrosetta.rosetta.protocols.denovo_design.components) find_pairing() (in module pyrosetta.rosetta.protocols.fldsgn.filters) find_pairing_idx() (in module pyrosetta.rosetta.protocols.fldsgn.filters) find_para_ion_position_and_compute_pre_score() (pyrosetta.rosetta.core.scoring.nmr.pre.PREMultiSet method) find_parallel() (pyrosetta.rosetta.protocols.features.strand_assembly.StrandBundleFeatures method) find_params_and_neighbors() (pyrosetta.rosetta.core.scoring.MultipoleElecPotential method) find_partner() (pyrosetta.rosetta.protocols.dna.DNAParameters method) find_peptide_attach_pt() (in module pyrosetta.rosetta.protocols.ligand_docking) find_pitch() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) find_pose_in_vector() (in module pyrosetta.rosetta.protocols.recon_design) find_positions() (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastFilter_nonmatching_prolines method) find_possible_disulfides() (pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover method) find_possible_orders() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) find_previously_loaded_fragmentStore() (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStoreManager method) find_relevant_connections_onersd() (in module pyrosetta.rosetta.core.scoring.methods) find_residue_max_radii() (in module pyrosetta.rosetta.core.pack) find_residues_on_chain1_inside_interface() (in module pyrosetta.rosetta.protocols.splice) find_resnum() (pyrosetta.rosetta.protocols.stepwise.sampler.copy_dofs.ResidueAlternativeStepWiseSamplerComb method) find_rosettascript_tag() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) find_rotation_center() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover method) find_satisfying_interactions_with_background() (in module pyrosetta.rosetta.core.pack.hbonds) find_seqpos_of_saccharides_child_residue_at() (in module pyrosetta.rosetta.core.conformation.carbohydrates) find_seqpos_of_saccharides_mainchain_child() (in module pyrosetta.rosetta.core.conformation.carbohydrates) find_seqpos_of_saccharides_parent_residue() (in module pyrosetta.rosetta.core.conformation.carbohydrates) find_sewable_region() (pyrosetta.rosetta.protocols.pose_sewing.movers.SewAnythingAddMover method) find_sheet() (in module pyrosetta.rosetta.protocols.features.strand_assembly) find_SilentStructOPs (class in pyrosetta.rosetta.protocols.wum) find_start_of_next_interface_region() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) find_starting_segment() (pyrosetta.rosetta.protocols.sewing.movers.AppendAssemblyMover method) (pyrosetta.rosetta.protocols.sewing.movers.LigandBindingAssemblyMover method) find_stop_of_this_interface_region() (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) FIND_SUGAR_AND_SUITE_FRAGS_I (pyrosetta.rosetta.basic.ProfTag attribute) FIND_SUGAR_AND_SUITE_FRAGS_II (pyrosetta.rosetta.basic.ProfTag attribute) find_symmetric_basejump_anchor() (in module pyrosetta.rosetta.core.pose.symmetry) find_symmetric_hbonds() (pyrosetta.rosetta.core.pack.hbonds.HBondGraphInitializerIG method) find_template() (in module pyrosetta.rosetta.protocols.tcr) find_template_from_multiple_input_db() (in module pyrosetta.rosetta.protocols.tcr) find_tm_regions() (pyrosetta.rosetta.protocols.protein_interface_design.movers.SecretionOptimizationMover method) find_type_matches() (pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore method) find_unconnected_residues() (in module pyrosetta.rosetta.protocols.ligand_docking) find_unsats() (pyrosetta.rosetta.protocols.hbnet.HBNet method) (pyrosetta.rosetta.protocols.hbnet.HBNetStapleInterface method) find_vl_vh_cut() (pyrosetta.rosetta.protocols.splice.RBInMover method) (pyrosetta.rosetta.protocols.splice.RBOutMover method) (pyrosetta.rosetta.protocols.splice.SpliceInAntibody method) (pyrosetta.rosetta.protocols.splice.SpliceOutAntibody method) find_weights_file() (in module pyrosetta.rosetta.core.scoring) find_whitespace() (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) find_zinc_site() (pyrosetta.rosetta.protocols.metal_interface.ZincSiteFinder method) findClusters() (pyrosetta.rosetta.protocols.pockets.CClusterSet method) (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PClusterSet method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findClustersByExemplars() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) FindConsensusSequence (class in pyrosetta.rosetta.protocols.recon_design) FindConsensusSequenceCreator (class in pyrosetta.rosetta.protocols.recon_design) findDecoyWithMostNeighbors() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) findEdgeId() (pyrosetta.rosetta.core.sequence.SequenceCoupling method) FindEndpointsOperation (class in pyrosetta.rosetta.protocols.splice) FindEndpointsOperationCreator (class in pyrosetta.rosetta.protocols.splice) findExemplars() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findLargestClusters() (pyrosetta.rosetta.protocols.cluster.calibur.Clustering method) findLoopFromDensity() (in module pyrosetta.rosetta.protocols.electron_density) findNeighors() (pyrosetta.rosetta.protocols.sparta.PDB method) findPockets() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) FindPossibleAtomTypesForAtom() (pyrosetta.rosetta.core.chemical.gasteiger.PossibleAtomTypesForAtom static method) findPSP() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findRoot() (pyrosetta.rosetta.protocols.pockets.SmallMol method) findSampling() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) findSampling5() (in module pyrosetta.rosetta.core.scoring.electron_density) (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) findSPS() (pyrosetta.rosetta.protocols.pockets.EggshellGrid method) (pyrosetta.rosetta.protocols.pockets.ElectrostaticpotentialGrid method) (pyrosetta.rosetta.protocols.pockets.PocketGrid method) (pyrosetta.rosetta.protocols.pockets.TargetPocketGrid method) findUU() (in module pyrosetta.rosetta.numeric.model_quality) fine_centering_mode (pyrosetta.rosetta.core.scoring.APBSConfig.I_PARAM property) fine_rmsd_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) finer_sampling_at_chain_closure() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) FingerprintBase (class in pyrosetta.rosetta.protocols.pockets) FingerprintMultifunc (class in pyrosetta.rosetta.protocols.pockets) finish_pose() (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) FINISHED (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) (pyrosetta.rosetta.protocols.monte_carlo.TrialResult attribute) finished() (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.AbstractArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase method) (pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive method) (pyrosetta.rosetta.protocols.jd2.archive.VarianceStatisticsArchive method) (pyrosetta.rosetta.protocols.symmetry.OrderedSequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.RandomSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SequentialSymmetrySlider method) (pyrosetta.rosetta.protocols.symmetry.SymmetrySlider method) finished_simulation() (pyrosetta.rosetta.protocols.canonical_sampling.AsyncMPITemperingBase method) (pyrosetta.rosetta.protocols.canonical_sampling.FixedTemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.HamiltonianExchange method) (pyrosetta.rosetta.protocols.canonical_sampling.ParallelTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.SimulatedTempering method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperatureController method) (pyrosetta.rosetta.protocols.canonical_sampling.TemperingBase method) finishPartialBond() (pyrosetta.rosetta.RDKit.RWMol method) finite() (pyrosetta.rosetta.core.scoring.PDvertex method) (pyrosetta.rosetta.core.scoring.power_diagram.PDvertex method) first (pyrosetta.CD property) (pyrosetta.rosetta.core.fragment.FragID property) First (pyrosetta.rosetta.protocols.indexed_structure_store.filters.LookupMode attribute) first() (pyrosetta.rosetta.protocols.match.Hit method) first_adjacent_heavy_atom() (pyrosetta.rosetta.core.conformation.Residue method) first_apply_with_current_setup_ (pyrosetta.rosetta.protocols.docking.DockingLowRes property) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble property) FIRST_ATOM_PROPERTY (pyrosetta.rosetta.core.chemical.AtomProperty attribute) first_base_atom() (in module pyrosetta.rosetta.core.chemical.rna) first_base_atom_index() (in module pyrosetta.rosetta.core.chemical.rna) first_beta2_aa (pyrosetta.rosetta.core.chemical.AA attribute) first_beta3_aa (pyrosetta.rosetta.core.chemical.AA attribute) first_connected_resonance() (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) first_D_aa (pyrosetta.rosetta.core.chemical.AA attribute) first_DNA_aa (pyrosetta.rosetta.core.chemical.AA attribute) first_l_aa (pyrosetta.rosetta.core.chemical.AA attribute) FIRST_LINK_TYPE (pyrosetta.rosetta.core.scoring.carbohydrates.CHIEnergyFunctionLinkageType attribute) first_node_is_donor() (pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo method) first_node_is_the_acceptor() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraphHbond method) first_oligourea (pyrosetta.rosetta.core.chemical.AA attribute) first_pass_ala_scan() (pyrosetta.rosetta.protocols.calc_taskop_filters.RotamerBoltzmannWeight method) first_pc (pyrosetta.rosetta.protocols.features.Segment property) FIRST_PROPERTY (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) first_res (pyrosetta.rosetta.basic.datacache.ResRotPair property) first_residue() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) first_residue_enzyme() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) first_residue_index() (pyrosetta.rosetta.core.conformation.parametric.Parameters method) (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters method) first_residue_substrate() (pyrosetta.rosetta.protocols.glycopeptide_docking.GlycopeptideDockingFlags method) first_rot (pyrosetta.rosetta.basic.datacache.ResRotPair property) first_sidechain_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) first_sidechain_hydrogen() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) FIRST_VARIANT (pyrosetta.rosetta.core.chemical.VariantType attribute) first_zero_pos() (pyrosetta.rosetta.protocols.canonical_sampling.mc_convergence_checks.HierarchicalLevel method) firstRes (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) firstResID (pyrosetta.rosetta.protocols.sparta.GDB property) fit_centered_coords() (in module pyrosetta.rosetta.protocols.toolbox) fit_layer_lines_with_splines() (in module pyrosetta.rosetta.core.energy_methods) fit_stdev() (pyrosetta.rosetta.core.scoring.epr_deer.metrics.DEERDecayData method) FIT_Tab (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) fitBfactors() (pyrosetta.rosetta.core.scoring.cryst.PhenixInterface method) FitBfactorsMover (class in pyrosetta.rosetta.protocols.cryst) FitBfactorsMoverCreator (class in pyrosetta.rosetta.protocols.cryst) fitFileName (pyrosetta.rosetta.protocols.sparta.Sparta.SpartaLib property) fitness() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) (pyrosetta.rosetta.protocols.multistate_design.SingleStateEntityData method) fitness_ (pyrosetta.rosetta.core.optimization.Particle property) fitness_function() (pyrosetta.rosetta.protocols.multistate_design.PackingState method) (pyrosetta.rosetta.protocols.multistate_design.SingleState method) fitness_function_ (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm property) fitness_pbest() (pyrosetta.rosetta.core.optimization.Particle method) fitness_threshold() (pyrosetta.rosetta.protocols.protein_interface_design.filters.BoltzmannFilter method) fitness_valid() (pyrosetta.rosetta.protocols.genetic_algorithm.Entity method) (pyrosetta.rosetta.protocols.multistate_design.MultiStateEntity method) fitnessCostPerATP() (pyrosetta.rosetta.protocols.evolution.AASynthesisFitnessCost method) FitnessFilter (class in pyrosetta.rosetta.protocols.recon_design) FitnessFilterCreator (class in pyrosetta.rosetta.protocols.recon_design) FitnessFunction (class in pyrosetta.rosetta.protocols.genetic_algorithm) FitSimpleHelix (class in pyrosetta.rosetta.protocols.helical_bundle) FitSimpleHelixCreator (class in pyrosetta.rosetta.protocols.helical_bundle) FitSimpleHelixMultiFunc (class in pyrosetta.rosetta.protocols.helical_bundle) FIVE_PRIME (pyrosetta.rosetta.core.pose.rna.Terminus attribute) five_prime_atom (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point property) five_prime_chain_break (pyrosetta.rosetta.protocols.stepwise.modeler.rna.sugar.SugarModeling property) five_prime_chain_break_res() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) FIVE_PRIME_END_OH (pyrosetta.rosetta.core.chemical.VariantType attribute) FIVE_PRIME_END_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) FIVE_PRIME_PACKABLE_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) FIVE_PRIME_PACKABLE_TRIPHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) FIVE_PRIME_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateTerminus attribute) five_prime_res() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker method) FIVE_PRIME_RME_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) five_prime_seq_num (pyrosetta.rosetta.protocols.stepwise.modeler.rna.Jump_point property) FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE (pyrosetta.rosetta.core.chemical.VariantType attribute) FIVEPRIME_CAP (pyrosetta.rosetta.core.chemical.VariantType attribute) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) fiveprime_cap() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) fix_bfactorsH() (in module pyrosetta.rosetta.core.scoring.cryst) fix_bfactorsMissing() (in module pyrosetta.rosetta.core.scoring.cryst) fix_chain_break_residue() (in module pyrosetta.rosetta.protocols.splice) fix_disulfides() (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) fix_glycan_order() (in module pyrosetta.rosetta.core.io) FIX_HIS_TAUTOMER (class in pyrosetta.rosetta.core.pack.task) fix_his_tautomer() (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) fix_pdbinfo_damaged_by_insertion() (in module pyrosetta.rosetta.core.pose) fix_protein_jump_atom() (in module pyrosetta.rosetta.protocols.stepwise.modeler) fix_reference_energies() (pyrosetta.rosetta.protocols.optimize_weights.OptEMultifunc method) fix_sugar_coords() (in module pyrosetta.rosetta.core.pose.rna) fix_tag_suffix() (in module pyrosetta.rosetta.protocols.toolbox) fix_tensor() (pyrosetta.rosetta.core.scoring.nmr.rdc.RDCMultiSet method) fix_tensors() (pyrosetta.rosetta.core.scoring.nmr.pcs.PCSMultiSet method) fix_up_jump_atoms() (in module pyrosetta.rosetta.protocols.stepwise.modeler) fix_up_jump_atoms_and_residue_type_variants() (in module pyrosetta.rosetta.protocols.stepwise.modeler) fix_up_residue_type_variants() (in module pyrosetta.rosetta.core.pose) fix_up_residue_type_variants_at_strand_beginning() (in module pyrosetta.rosetta.core.pose) fix_up_residue_type_variants_at_strand_end() (in module pyrosetta.rosetta.core.pose) fix_with_coord_cst() (in module pyrosetta.rosetta.protocols.loops) fix_worst_bad_ramas() (in module pyrosetta.rosetta.protocols.relax) FixAllLoopsMover (class in pyrosetta.rosetta.protocols.pose_length_moves) FixAllLoopsMoverCreator (class in pyrosetta.rosetta.protocols.pose_length_moves) FixbbCoupledRotamerSimAnnealer (class in pyrosetta.rosetta.core.pack.annealer) FixbbLinkingRotamerSimAnnealer (class in pyrosetta.rosetta.core.pack.annealer) FixbbPwatSimAnnealer (class in pyrosetta.rosetta.core.pack.annealer) FixbbRotamerSets (class in pyrosetta.rosetta.core.pack.rotamer_set) FixbbSimAnnealer (class in pyrosetta.rosetta.core.pack.annealer) FIXED (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation attribute) (pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerSpecificationType attribute) fixed() (pyrosetta.rosetta.core.scoring.OneToAllEnergyContainer method) fixed_data() (pyrosetta.rosetta.protocols.optimize_weights.PNatAAOptERotamerData method) (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData method) (pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData method) fixed_dist() (pyrosetta.rosetta.core.scoring.RDC method) (pyrosetta.rosetta.core.scoring.RDC_Rohl method) FIXED_DOMAIN (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameterType attribute) fixed_domain_map() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) fixed_energies() (pyrosetta.rosetta.core.scoring.MinimizationGraph method) fixed_energy_terms() (pyrosetta.rosetta.protocols.optimize_weights.OptEData method) fixed_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) fixed_size() (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 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) fixed_stems() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) FixedBBEdge (class in pyrosetta.rosetta.core.pack.interaction_graph) FixedBBInteractionGraph (class in pyrosetta.rosetta.core.pack.interaction_graph) FixedBBNode (class in pyrosetta.rosetta.core.pack.interaction_graph) FixedOffsetPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) FixedOffsetsPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) FixedPivots (class in pyrosetta.rosetta.protocols.kinematic_closure.pivot_pickers) fixedsizearray0_double_3_t (class in pyrosetta.rosetta.utility) fixedsizearray0_double_5_t (class in pyrosetta.rosetta.utility) fixedsizearray0_utility_fixedsizearray0_double_3_3_t (class in pyrosetta.rosetta.utility) fixedsizearray0_utility_fixedsizearray0_double_5_5_t (class in pyrosetta.rosetta.utility) fixedsizearray1_bool_1_t (class in pyrosetta.rosetta.utility) fixedsizearray1_bool_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_bool_3_t (class in pyrosetta.rosetta.utility) fixedsizearray1_bool_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_bool_5_t (class in pyrosetta.rosetta.utility) fixedsizearray1_bool_6_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepNRChiSample_float_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_1_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_2_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_3_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_4_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_BBDepScoreInterpData_5_64_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_1_float_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_2_float_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_3_float_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_4_float_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_1_5_float_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_1_float_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_2_float_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_3_float_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_4_float_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_2_5_float_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_1_float_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_2_float_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_3_float_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_4_float_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_3_5_float_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_1_float_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_2_float_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_3_float_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_4_float_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_4_5_float_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_1_float_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_2_float_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_3_float_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_4_float_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_core_pack_dunbrack_PackedDunbrackRotamer_5_5_float_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_1_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_3_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_5_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_64_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_6_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_7_t (class in pyrosetta.rosetta.utility) fixedsizearray1_double_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_float_1_t (class in pyrosetta.rosetta.utility) fixedsizearray1_float_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_float_3_t (class in pyrosetta.rosetta.utility) fixedsizearray1_float_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_float_5_t (class in pyrosetta.rosetta.utility) fixedsizearray1_int_3_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_interpolation_CatmullRomSplineBoundaryType_1_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_interpolation_CatmullRomSplineBoundaryType_6_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_interpolation_spline_BorderFlag_1_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_interpolation_spline_BorderFlag_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_interpolation_spline_BorderFlag_3_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_interpolation_spline_BorderFlag_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_interpolation_spline_BorderFlag_5_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_interpolation_spline_BorderFlag_6_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathNTensor_double_1_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathNTensor_double_2_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathNTensor_double_3_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathNTensor_double_4_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathNTensor_double_5_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathNTensor_double_6_64_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathVector_double_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathVector_double_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathVector_double_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_numeric_MathVector_double_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_ObjexxFCL_FArray1D_double_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_ObjexxFCL_FArray1D_double_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_ObjexxFCL_FArray1D_double_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_ObjexxFCL_FArray1D_double_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_ObjexxFCL_FArray1D_double_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_protocols_match_ProbeRadius_3_t (class in pyrosetta.rosetta.utility) fixedsizearray1_std_pair_double_double_1_t (class in pyrosetta.rosetta.utility) fixedsizearray1_std_pair_double_double_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_std_pair_double_double_3_t (class in pyrosetta.rosetta.utility) fixedsizearray1_std_pair_double_double_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_std_pair_double_double_5_t (class in pyrosetta.rosetta.utility) fixedsizearray1_std_pair_double_double_6_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_char_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_char_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_1_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_3_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_5_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_6_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_7_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_long_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_unsigned_short_6_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_fixedsizearray1_double_16_16_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_fixedsizearray1_double_2_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_fixedsizearray1_double_32_32_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_fixedsizearray1_double_4_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_fixedsizearray1_double_5_5_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_fixedsizearray1_double_64_64_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_fixedsizearray1_double_8_8_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_1_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_2_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_3_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_4_t (class in pyrosetta.rosetta.utility) fixedsizearray1_utility_vector1_unsigned_long_std_allocator_unsigned_long_5_t (class in pyrosetta.rosetta.utility) FixedTemperatureController (class in pyrosetta.rosetta.protocols.canonical_sampling) fixEigenvector() (in module pyrosetta.rosetta.numeric.model_quality) fixH() (in module pyrosetta.rosetta.protocols.relax) fixResidue() (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSingle method) FixTemplateJumpSetup (class in pyrosetta.rosetta.protocols.abinitio) fixup_magnesiums() (in module pyrosetta.rosetta.protocols.magnesium) fixup_patches() (in module pyrosetta.rosetta.core.chemical) Fl (pyrosetta.rosetta.core.chemical.element.Elements attribute) flag_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) flag_for_calculation() (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo method) flag_for_calculation_ (pyrosetta.rosetta.core.scoring.facts.FACTSResidueInfo property) flags() (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.std.ios_base method) flags_and_objects_are_in_sync_ (pyrosetta.rosetta.protocols.docking.DockingLowRes property) (pyrosetta.rosetta.protocols.docking.DockingLowResEnsemble property) flank_residue_min() (pyrosetta.rosetta.protocols.loops.loop_mover.refine.LoopMover_Refine_CCD method) flanking_left_aa() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_left_nres() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_left_ss() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_right_aa() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_right_nres() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) flanking_right_ss() (pyrosetta.rosetta.protocols.forge.build.SegmentInsert method) FLAT (pyrosetta.rosetta.numeric.interpolation.CatmullRomSplineBoundaryType attribute) flat_d_aa_ramatable (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) flat_d_aa_ramatable_stringent (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) flat_l_aa_ramatable (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) flat_l_aa_ramatable_stringent (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) flat_size() (pyrosetta.rosetta.core.fragment.FrameList method) flat_symm_dl_aa_ramatable (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) flat_symm_dl_aa_ramatable_stringent (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) flat_symm_gly_ramatable (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) flat_symm_gly_ramatable_stringent (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) flat_symm_pro_ramatable (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) flat_symm_pro_ramatable_stringent (pyrosetta.rosetta.core.scoring.Rama_Table_Type attribute) FlatHarmonicFunc (class in pyrosetta.rosetta.core.scoring.func) Flavodoxin (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldType attribute) flexbb() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) FlexBBDesignMeanField (class in pyrosetta.rosetta.protocols.mean_field) FlexbbEdge (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) FlexbbIGFactory (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) FlexbbInteractionGraph (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) FlexbbInteractionGraph.Subsitution (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) FlexBBMeanField (class in pyrosetta.rosetta.protocols.mean_field) FlexbbNode (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) FlexbbRotamerSet (class in pyrosetta.rosetta.protocols.flexpack.rotamer_set) FlexbbRotamerSets (class in pyrosetta.rosetta.protocols.flexpack.rotamer_set) FlexbbSimAnnealer (class in pyrosetta.rosetta.protocols.flexpack.annealer) FlexbbSparseMatrixIndex (class in pyrosetta.rosetta.protocols.flexpack.interaction_graph) flexible_label() (pyrosetta.rosetta.protocols.fold_from_loops.utils.Nub static method) flexpack_neighbor_graph() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) FlexPacker (class in pyrosetta.rosetta.protocols.flexpack) FlexPepDockingAbInitio (class in pyrosetta.rosetta.protocols.flexpep_docking) FlexPepDockingFlags (class in pyrosetta.rosetta.protocols.flexpep_docking) FlexPepDockingLowRes (class in pyrosetta.rosetta.protocols.flexpep_docking) FlexPepDockingPoseMetrics (class in pyrosetta.rosetta.protocols.flexpep_docking) FlexPepDockingProtocol (class in pyrosetta.rosetta.protocols.flexpep_docking) FlexPepDockingProtocolCreator (class in pyrosetta.rosetta.protocols.flexpep_docking) flexseg_members() (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) flexsegid_for_moltenres() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) flexsegid_for_res() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) flexsegment_size() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) flexsegment_start_moltenresid() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) flexsegment_start_resid() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) flexsegment_stop_moltenresid() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) flexsegment_stop_resid() (pyrosetta.rosetta.protocols.flexpack.rotamer_set.FlexbbRotamerSets method) flip_atom_xyz() (in module pyrosetta.rosetta.core.io.pose_from_sfr) FLIP_CHIRALITY (pyrosetta.rosetta.protocols.simple_moves.chiral.Chirality attribute) flip_HNQ() (pyrosetta.rosetta.core.pack.task.operation.OptH method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) flip_subset() (pyrosetta.rosetta.core.pack.task.operation.OperateOnResidueSubset method) flip_upstream_downstream_samples() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.ExternalGeomSampler method) FlipChiralityMover (class in pyrosetta.rosetta.protocols.cyclic_peptide) FlipChiralityMoverCreator (class in pyrosetta.rosetta.protocols.cyclic_peptide) FlipMover (class in pyrosetta.rosetta.protocols.membrane) FlipMoverCreator (class in pyrosetta.rosetta.protocols.membrane) flipped() (pyrosetta.rosetta.core.pose.rna.BasePair method) (pyrosetta.rosetta.core.pose.rna.BaseStack method) float4 (class in pyrosetta.rosetta.basic.gpu) float_ambiguity() (pyrosetta.rosetta.protocols.noesy_assign.PeakAssignment method) float_label() (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) float_of() (in module pyrosetta.rosetta.ObjexxFCL) (pyrosetta.rosetta.ObjexxFCL.Fstring method) (pyrosetta.rosetta.ObjexxFCL.Fsubstring method) floating_base() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) floating_base_anchor_res() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) FloatingResonance (class in pyrosetta.rosetta.protocols.noesy_assign) flood_fill3D() (in module pyrosetta.rosetta.protocols.sic_dock) FloppyTailMover (class in pyrosetta.rosetta.protocols.floppy_tail) FLORECENCE_TRANSFER (pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique attribute) floyd_warshall() (pyrosetta.rosetta.core.chemical.VDDistanceMatrix method) FLUORO_SUGAR (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) flush() (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.Emitter method) (pyrosetta.rosetta.basic.JsonEmitter method) (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.MemTracer.TracerProxy method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.MemTracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.PyTracer method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.Tracer.TracerProxy method) (pyrosetta.rosetta.basic.TracerImpl method) (pyrosetta.rosetta.basic.TracerImpl.TracerProxyImpl method) (pyrosetta.rosetta.basic.TracerToFile method) (pyrosetta.rosetta.basic.YamlEmitter method) (pyrosetta.rosetta.protocols.dna.PDBOutput method) (pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter method) (pyrosetta.rosetta.protocols.features.DatabaseJobOutputter method) (pyrosetta.rosetta.protocols.frag_picker.QuotaDebug method) (pyrosetta.rosetta.protocols.jd2.AtomTreeDiffJobOutputter method) (pyrosetta.rosetta.protocols.jd2.FileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.JobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmCIFJobOutputter method) (pyrosetta.rosetta.protocols.jd2.mmtfJobOutputter method) (pyrosetta.rosetta.protocols.jd2.NoOutputJobOutputter method) (pyrosetta.rosetta.protocols.jd2.PDBJobOutputter method) (pyrosetta.rosetta.protocols.jd2.RNA_DeNovoJobOutputter method) (pyrosetta.rosetta.protocols.jd2.ScoreOnlyJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SerializedPoseJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SilentFileJobOutputter method) (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.protocols.jd2.WriteFileSFB method) (pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter method) (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.output.MultipleOutputter method) (pyrosetta.rosetta.protocols.jd3.output.ResultOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.DeNovoSilentFilePoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.mmTFPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PDBPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.PoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.ScoreFileOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SecondaryPoseOutputter method) (pyrosetta.rosetta.protocols.jd3.pose_outputters.SilentFilePoseOutputter 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) (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.mpi_stream.basic_mpi_streambuf_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) flush_all_channels() (pyrosetta.rosetta.basic.MemTracer method) (pyrosetta.rosetta.basic.MemTracerImpl method) (pyrosetta.rosetta.basic.Tracer method) (pyrosetta.rosetta.basic.TracerImpl method) flush_checkpoints() (pyrosetta.rosetta.protocols.checkpoint.CheckPointer method) flush_final() (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) flush_finalize() (pyrosetta.rosetta.utility.io.ozstream method) FlxbbDesign (class in pyrosetta.rosetta.protocols.flxbb) FlxbbDesign_main() (in module pyrosetta.rosetta.protocols.flxbb) FlxbbDesignCreator (class in pyrosetta.rosetta.protocols.flxbb) FlxbbDesignPack (class in pyrosetta.rosetta.protocols.flxbb) Fm (pyrosetta.rosetta.core.chemical.element.Elements attribute) fmt_real() (in module pyrosetta.rosetta.utility) fname() (pyrosetta.rosetta.core.pose.RID_FileSource method) (pyrosetta.rosetta.protocols.simple_moves.AddChainMover method) fname_initialized_from() (pyrosetta.rosetta.core.pack.task.ResfileContents method) FNatFilter (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) FNatFilterCreator (class in pyrosetta.rosetta.protocols.protein_interface_design.filters) fnorm (pyrosetta.rosetta.numeric.nls.lm_status_struct property) fobjnames() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) focused_edge() (pyrosetta.rosetta.core.pack.guidance_scoreterms.buried_unsat_penalty.graph.BuriedUnsatPenaltyGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.NPDHBSimpleInteractionGraph method) (pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph method) (pyrosetta.rosetta.core.scoring.constraints.ConstraintGraph method) (pyrosetta.rosetta.core.scoring.ContextGraph method) (pyrosetta.rosetta.core.scoring.EnergyGraph method) (pyrosetta.rosetta.core.scoring.MinimizationGraph method) (pyrosetta.rosetta.core.scoring.TenANeighborGraph method) (pyrosetta.rosetta.core.scoring.TwelveANeighborGraph 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) fold() (pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication method) fold_in_rb_deltas() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) fold_label_resonance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) fold_proton_resonance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeakInfo method) fold_resonance() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) fold_tree() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation 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.ScoreJumpFileSilentStruct method) (pyrosetta.rosetta.core.pose.MiniPose method) (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph method) (pyrosetta.rosetta.protocols.environment.ProtectedConformation method) (pyrosetta.rosetta.protocols.jumping.JumpSample method) (pyrosetta.rosetta.protocols.protein_interface_design.movers.SetAtomTree method) (pyrosetta.rosetta.protocols.rigid.RigidBodyMotionMover method) (pyrosetta.rosetta.protocols.seeded_abinitio.SeedFoldTree method) (pyrosetta.rosetta.protocols.splice.Splice method) (pyrosetta.rosetta.protocols.splice.SpliceManager method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) fold_tree_from_loops() (in module pyrosetta.rosetta.protocols.forge.methods) (in module pyrosetta.rosetta.protocols.loops) fold_tree_from_pose() (in module pyrosetta.rosetta.protocols.forge.methods) fold_tree_from_silent_file() (pyrosetta.rosetta.core.import_pose.RNA_DeNovoParameters method) fold_tree_io() (pyrosetta.rosetta.core.import_pose.ImportPoseOptions method) (pyrosetta.rosetta.core.io.StructFileReaderOptions method) (pyrosetta.rosetta.core.io.StructFileRepOptions method) FoldandDockClaimer (class in pyrosetta.rosetta.protocols.topology_broker) FoldArchitectMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) FoldArchitectMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) FoldConstraints (class in pyrosetta.rosetta.protocols.abinitio) FoldConstraints.StageID (class in pyrosetta.rosetta.protocols.abinitio) folder() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D method) FoldGraph (class in pyrosetta.rosetta.protocols.denovo_design.components) foldInChanges() (pyrosetta.rosetta.protocols.electron_density.VoxelSpacingMultifunc method) FoldResonance (class in pyrosetta.rosetta.protocols.noesy_assign) FoldTree (class in pyrosetta.rosetta.core.kinematics) foldTree() (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) foldtree_string() (pyrosetta.rosetta.core.io.StructFileRep method) FoldTreeFromFoldGraphMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) FoldTreeFromFoldGraphMoverCreator (class in pyrosetta.rosetta.protocols.denovo_design.movers) FoldTreeFromLoops (class in pyrosetta.rosetta.protocols.loops) FoldTreeFromLoopsCreator (class in pyrosetta.rosetta.protocols.loops) FoldTreeFromMotif (class in pyrosetta.rosetta.protocols.simple_moves) FoldTreeFromMotifCreator (class in pyrosetta.rosetta.protocols.simple_moves) FoldTreeHybridize (class in pyrosetta.rosetta.protocols.hybridization) FoldTreeRequest (class in pyrosetta.rosetta.protocols.loop_modeling) FoldTreeSketch (class in pyrosetta.rosetta.core.environment) FoldTreeSketch.Node (class in pyrosetta.rosetta.core.environment) foldtype_from_name() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) foldtype_from_spairs() (pyrosetta.rosetta.protocols.fldsgn.topology.SheetFoldTypeManager method) follow_edge() (pyrosetta.rosetta.protocols.legacy_sewing.Assembly method) (pyrosetta.rosetta.protocols.legacy_sewing.ContinuousAssembly method) (pyrosetta.rosetta.protocols.legacy_sewing.DisembodiedAssembly method) follow_EX_flags (pyrosetta.rosetta.protocols.match.upstream.ChiStrategy attribute) follow_random_edge_from_node() (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) foo_all() (in module pyrosetta.rosetta.utility.py) foo_all_sp() (in module pyrosetta.rosetta.utility.py) foo_int() (pyrosetta.rosetta.utility.py.Base method) foo_string() (pyrosetta.rosetta.utility.py.Base method) foo_value() (pyrosetta.rosetta.utility.py.Base method) foo_value_sp() (pyrosetta.rosetta.utility.py.Base method) footprint() (pyrosetta.rosetta.utility.graph.ArrayPool_double_t method) forbidden_aas() (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDesignOperation method) force (pyrosetta.rosetta.protocols.cartesian.CartesianAtom property) (pyrosetta.rosetta.protocols.ligand_docking.Translate_info property) force_aa_neighbors() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) force_aa_neighbors_for_edge() (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.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) force_all_aa_neighbors() (pyrosetta.rosetta.core.pack.hbonds.BareMinimumPDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.AminoAcidNeighborSparseMatrix_float_t method) (pyrosetta.rosetta.core.pack.interaction_graph.DensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleDensePDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FASTEREdge method) (pyrosetta.rosetta.core.pack.interaction_graph.FixedBBEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LazyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.LinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.OnTheFlyEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PDEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.PrecomputedPairEnergiesEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmLinearMemEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmMinimalistEdge method) (pyrosetta.rosetta.core.pack.interaction_graph.SymmOnTheFlyEdge method) force_all_aa_neighbors_for_edge() (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.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) force_anti_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) force_bitflip() (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) force_centroid_interaction() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) force_combined_gaussian_approximation() (pyrosetta.rosetta.core.scoring.func.GaussianChainFunc method) force_commit_transaction() (pyrosetta.rosetta.utility.sql_database.session method) force_const() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) FORCE_EXISTING_BASE_TYPE (pyrosetta.rosetta.core.pack.palette.SpecialPackerPaletteBehaviour attribute) force_fold_tree() (pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna.StepWiseWorkingParametersSetup method) force_job_purging() (pyrosetta.rosetta.protocols.jd2.JobsContainer method) force_moving_res_for_erraser() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) force_natro() (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) (pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator method) force_natro_for_stored_task_names() (pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover method) force_nbr_atom_orient() (pyrosetta.rosetta.core.chemical.MutableResidueType method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.ResidueTypeBase method) force_next_move_reject() (pyrosetta.rosetta.protocols.moves.SimulatedTempering method) force_north_sugar_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) force_phosphate_instantiation() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseRNA_ModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.MultiPhosphateSampler method) (pyrosetta.rosetta.protocols.stepwise.modeler.rna.phosphate.PhosphateMover method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) force_silent_bitflip_on_read() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) force_silent_bitflip_on_read_set() (pyrosetta.rosetta.core.io.silent.SilentFileOptions method) force_south_sugar_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) force_stub_intra_residue (pyrosetta.rosetta.protocols.environment.claims.JumpElement property) force_submotif_without_intervening_bulge() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) force_syn_chi_res_list() (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) force_total_rounds() (pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler method) force_unique_moves() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.StepWiseMoveSelector method) ForceDisulfidesMover (class in pyrosetta.rosetta.protocols.calc_taskop_movers) ForceDisulfidesMoverCreator (class in pyrosetta.rosetta.protocols.calc_taskop_movers) ForeignKey (class in pyrosetta.rosetta.basic.database.schema_generator) forget_chains_and_interface() (pyrosetta.rosetta.protocols.dna.RestrictDesignToProteinDNAInterface method) forget_initial_loops() (pyrosetta.rosetta.protocols.anchored_design.AnchoredDesignMover method) form_disulfide() (in module pyrosetta.rosetta.core.conformation) form_disulfide_helper() (in module pyrosetta.rosetta.core.conformation) formal_charge() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.chemical.sdf.MolFileIOAtom method) formalcharge (pyrosetta.rosetta.core.io.AtomInformation property) FORMAT (pyrosetta.rosetta.protocols.sparta.GDB property) FORMAT_str (pyrosetta.rosetta.protocols.sparta.GDB property) FORMAT_str_parser() (pyrosetta.rosetta.protocols.sparta.GDB method) formatted_icoord_tree() (in module pyrosetta.rosetta.core.chemical) formatted_objs_names() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) formatted_objs_values() (pyrosetta.rosetta.protocols.mpi_refinement.MultiObjective method) FormFactor (class in pyrosetta.rosetta.core.scoring.saxs) FormFactorManager (class in pyrosetta.rosetta.core.scoring.saxs) FORMUL (pyrosetta.rosetta.core.io.pdb.RecordType attribute) forward (pyrosetta.rosetta.protocols.carbohydrates.QuenchDirection attribute) (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.ChainDirection attribute) forward_check() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) forward_connections() (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) forward_jump() (pyrosetta.rosetta.protocols.motifs.Motif method) (pyrosetta.rosetta.protocols.motifs.SingleMotif method) found_centroid_interaction() (pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker method) found_match (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookupResult property) found_move() (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) FourAtomsConstraintData (class in pyrosetta.rosetta.protocols.frag_picker.scores) FourPointsFunc (class in pyrosetta.rosetta.core.scoring.func) fp_compare() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) fp_compare_deriv() (pyrosetta.rosetta.protocols.pockets.PlaidFingerprint method) fpos___mbstate_t_t (class in pyrosetta.rosetta.std) Fr (pyrosetta.rosetta.core.chemical.element.Elements attribute) fr (pyrosetta.rosetta.protocols.tcr.TCRmodel.tcrtmplts property) (pyrosetta.rosetta.protocols.tcr.TCRseqInfo.tcrsegs property) fr1 (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr1_begin (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr1_end (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr2 (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr2_begin (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr2_end (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr3 (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr3_begin (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr3_end (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr4 (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChainNumbering property) (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr4_begin (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) fr4_end (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyFramework property) frac() (pyrosetta.rosetta.core.scoring.elec.electrie.ElecAtom method) frac_atoms_within() (in module pyrosetta.rosetta.protocols.ligand_docking) frac_cav_ball_required_exposed (pyrosetta.rosetta.core.scoring.packstat.SasaOptions property) fract_property_penalty() (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup method) fraction_by_recombination() (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithm method) (pyrosetta.rosetta.protocols.genetic_algorithm.GeneticAlgorithmBase method) fraction_hydrophobic_sasa() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) fraction_polar_sasa() (pyrosetta.rosetta.protocols.cyclic_peptide_predict.HierarchicalHybridJD_SASASummary method) FractionSelector (class in pyrosetta.rosetta.core.select.residue_selector) FractionSelectorCreator (class in pyrosetta.rosetta.core.select.residue_selector) frag3_weight (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) frag5_weight (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) frag9_weight (pyrosetta.rosetta.protocols.flexpep_docking.FlexPepDockingFlags property) frag_cache_ (pyrosetta.rosetta.protocols.simple_moves.GunnCost property) frag_files() (pyrosetta.rosetta.protocols.indel.IndelOptimizationMover method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseProteinModelerOptions method) frag_id() (pyrosetta.rosetta.core.fragment.FragID_Iterator method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) frag_libs() (pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover method) (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover method) (pyrosetta.rosetta.protocols.loop_build.LoopMover_SlidingWindow method) (pyrosetta.rosetta.protocols.loops.loop_mover.IndependentLoopMover 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.relax.loop.LoopRelaxMover method) frag_num (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover.Item property) frag_set_loader_ct_namer() (pyrosetta.rosetta.protocols.parser.FragSetLoader static method) frag_size() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) (pyrosetta.rosetta.protocols.frags.TorsionFragmentMover method) (pyrosetta.rosetta.protocols.rna.denovo.movers.RNA_DeNovoMasterMover method) frag_sizes() (pyrosetta.rosetta.protocols.frags.FragLib method) frag_sizes_ (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker property) frag_type() (pyrosetta.rosetta.core.fragment.FragFactory method) fragbias_reporter() (pyrosetta.rosetta.protocols.hybridization.FragmentBiasAssigner method) FragCache_protocols_simple_moves_GunnTuple_t (class in pyrosetta.rosetta.core.fragment) FragData (class in pyrosetta.rosetta.core.fragment) fragDens_ (pyrosetta.rosetta.protocols.electron_density.SelectDensityPointsOptions property) FragFactory (class in pyrosetta.rosetta.core.fragment) FragID (class in pyrosetta.rosetta.core.fragment) fragID() (pyrosetta.rosetta.core.fragment.FrameList method) FragID_Iterator (class in pyrosetta.rosetta.core.fragment) FragInsertAndAlignMover (class in pyrosetta.rosetta.protocols.rbsegment_relax) FragLib (class in pyrosetta.rosetta.protocols.frags) FRAGMENT (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) (pyrosetta.rosetta.core.io.HeaderInformation attribute) (pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken attribute) fragment() (pyrosetta.rosetta.core.fragment.FragID method) (pyrosetta.rosetta.core.fragment.FragmentRmsd method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) fragment_1 (pyrosetta.rosetta.protocols.features.helixAssembly.FragmentPair property) fragment_2 (pyrosetta.rosetta.protocols.features.helixAssembly.FragmentPair property) fragment_as_pose() (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) fragment_atoms (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification property) fragment_contacts() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) fragment_coordinates (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore property) fragment_length (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentSpecification property) FRAGMENT_MOVER (pyrosetta.rosetta.basic.ProfTag attribute) fragment_ptr() (pyrosetta.rosetta.core.fragment.FragID method) (pyrosetta.rosetta.core.fragment.Frame method) (pyrosetta.rosetta.core.fragment.JumpingFrame method) (pyrosetta.rosetta.core.fragment.NonContinuousFrame method) (pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion method) fragment_set_slice() (in module pyrosetta.rosetta.core.fragment) fragment_specification (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore property) fragment_specification() (pyrosetta.rosetta.protocols.indexed_structure_store.filters.FragmentLookupFilter method) (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentLookup method) fragment_threshold_distances (pyrosetta.rosetta.protocols.indexed_structure_store.FragmentStore property) FragmentAllAtomCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentBiasAssigner (class in pyrosetta.rosetta.protocols.hybridization) FragmentCandidate (class in pyrosetta.rosetta.protocols.frag_picker) FragmentChunkCrms (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentClaimer (class in pyrosetta.rosetta.protocols.topology_broker) FragmentCM (class in pyrosetta.rosetta.protocols.abinitio.abscript) FragmentCMCreator (class in pyrosetta.rosetta.protocols.abinitio.abscript) FragmentComparatorBase (class in pyrosetta.rosetta.protocols.frag_picker) FragmentCost (class in pyrosetta.rosetta.protocols.simple_moves) FragmentCrmsd (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentCrmsdResDepth (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentDME (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentExtension (class in pyrosetta.rosetta.protocols.loop_grower) FragmentExtensionCreator (class in pyrosetta.rosetta.protocols.loop_grower) FragmentIO (class in pyrosetta.rosetta.core.fragment) FragmentJumpClaimer (class in pyrosetta.rosetta.protocols.topology_broker) FragmentJumpCM (class in pyrosetta.rosetta.protocols.abinitio.abscript) FragmentJumpCMCreator (class in pyrosetta.rosetta.protocols.abinitio.abscript) FragmentLibrary (class in pyrosetta.rosetta.core.fragment.rna) FragmentLibraryManager (class in pyrosetta.rosetta.core.fragment.picking_old) FragmentLookup (class in pyrosetta.rosetta.protocols.indexed_structure_store) FragmentLookupFilter (class in pyrosetta.rosetta.protocols.indexed_structure_store.filters) FragmentLookupFilterCreator (class in pyrosetta.rosetta.protocols.indexed_structure_store.filters) FragmentLookupResult (class in pyrosetta.rosetta.protocols.indexed_structure_store) FragmentMover (class in pyrosetta.rosetta.protocols.simple_moves) FragmentPair (class in pyrosetta.rosetta.protocols.features.helixAssembly) FragmentPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) FragmentPicker (class in pyrosetta.rosetta.protocols.frag_picker) FRAGMENTPICKING (pyrosetta.rosetta.basic.ProfTag attribute) FRAGMENTPICKING_ATOMPAIR_SCORE (pyrosetta.rosetta.basic.ProfTag attribute) FRAGMENTPICKING_CANDIDATES_COLLECTING (pyrosetta.rosetta.basic.ProfTag attribute) FRAGMENTPICKING_CS_SCORE (pyrosetta.rosetta.basic.ProfTag attribute) FRAGMENTPICKING_DIHEDRALCONSTR_SCORE (pyrosetta.rosetta.basic.ProfTag attribute) FRAGMENTPICKING_PHIPSI_SCORE (pyrosetta.rosetta.basic.ProfTag attribute) FRAGMENTPICKING_PROFILE_CAHING (pyrosetta.rosetta.basic.ProfTag attribute) FRAGMENTPICKING_PROFILE_SCORE (pyrosetta.rosetta.basic.ProfTag attribute) FRAGMENTPICKING_READ_VALL (pyrosetta.rosetta.basic.ProfTag attribute) FRAGMENTPICKING_SECONDARY_SCORE (pyrosetta.rosetta.basic.ProfTag attribute) FragmentReader (class in pyrosetta.rosetta.protocols.parser) FragmentRmsd (class in pyrosetta.rosetta.core.fragment) fragments() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrarian method) (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover 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.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.FragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.ResTypeFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) fragments_for_permutation() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) fragments_for_permutation_take_X_from_pose() (pyrosetta.rosetta.protocols.denovo_design.components.Picker method) fragments_id() (pyrosetta.rosetta.protocols.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) FragmentSampler (class in pyrosetta.rosetta.protocols.abinitio) FragmentScoreFilter (class in pyrosetta.rosetta.protocols.frag_picker) FragmentScoreFilterCreator (class in pyrosetta.rosetta.protocols.frag_picker) FragmentScoreManager (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentScoreMap (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentScoringMethod (class in pyrosetta.rosetta.protocols.frag_picker.scores) FragmentSelectingRule (class in pyrosetta.rosetta.protocols.frag_picker) FragmentSetLoader (class in pyrosetta.rosetta.core.fragment) FragmentSetLoaderCreator (class in pyrosetta.rosetta.core.fragment) FragmentSpecification (class in pyrosetta.rosetta.protocols.indexed_structure_store) FragmentStore (class in pyrosetta.rosetta.protocols.indexed_structure_store) FragmentStoreManager (class in pyrosetta.rosetta.protocols.indexed_structure_store) FragmentStoreProvider (class in pyrosetta.rosetta.protocols.indexed_structure_store) FragQualCalculator (class in pyrosetta.rosetta.protocols.pose_metric_calculators) FragQualFilter (class in pyrosetta.rosetta.protocols.fldsgn.filters) FragQualFilterCreator (class in pyrosetta.rosetta.protocols.fldsgn.filters) frags_per_pos() (pyrosetta.rosetta.protocols.frag_picker.BestTotalScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.CompositeFragmentSelector method) (pyrosetta.rosetta.protocols.frag_picker.CustomScoreSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdByClustering method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyCrmsdSelector method) (pyrosetta.rosetta.protocols.frag_picker.DiversifyDihedralsSelector method) (pyrosetta.rosetta.protocols.frag_picker.FragmentSelectingRule method) (pyrosetta.rosetta.protocols.frag_picker.quota.QuotaSelector method) FragSet (class in pyrosetta.rosetta.core.fragment) FragSetCollection (class in pyrosetta.rosetta.core.fragment) FragSetLoader (class in pyrosetta.rosetta.protocols.parser) FragSetLoaderCreator (class in pyrosetta.rosetta.protocols.parser) FragsToAtomDist (class in pyrosetta.rosetta.protocols.noesy_assign) FragsToAtomDist.DistanceRecord (class in pyrosetta.rosetta.protocols.noesy_assign) Frame (class in pyrosetta.rosetta.core.fragment) frame() (pyrosetta.rosetta.core.fragment.FragFactory method) (pyrosetta.rosetta.core.fragment.FragID method) (pyrosetta.rosetta.protocols.kinematic_closure.ClosureProblem method) (pyrosetta.rosetta.protocols.match.upstream.FullChiSampleSet method) frame_from_global_orientation() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.LigandConformer method) frame_pos (pyrosetta.rosetta.protocols.simple_moves.LoggedFragmentMover.Item property) frame_ptr() (pyrosetta.rosetta.core.fragment.ConstFrameIterator method) (pyrosetta.rosetta.core.fragment.FragID method) (pyrosetta.rosetta.core.fragment.FrameIterator method) frame_vector() (pyrosetta.rosetta.core.fragment.FrameList method) FrameIterator (class in pyrosetta.rosetta.core.fragment) FrameIteratorWorker_ (class in pyrosetta.rosetta.core.fragment) FrameList (class in pyrosetta.rosetta.core.fragment) FrameListIterator_ (class in pyrosetta.rosetta.core.fragment) frames() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.FragSetCollection method) (pyrosetta.rosetta.core.fragment.MinimalFragSet method) (pyrosetta.rosetta.core.fragment.OrderedFragSet method) FrameWork (class in pyrosetta.rosetta.protocols.antibody) framework_dependant_clusters() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) framework_dependant_mutations() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) framework_dependant_positions() (pyrosetta.rosetta.protocols.antibody.design.MutateFrameworkForCluster method) framework_region (pyrosetta.rosetta.protocols.antibody.AntibodyRegionEnum attribute) free_2HOprime (pyrosetta.rosetta.core.scoring.ScoreType attribute) free_2HOprime_bonus() (pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options method) free_base (pyrosetta.rosetta.core.scoring.ScoreType attribute) free_data() (pyrosetta.rosetta.protocols.optimize_weights.PNatRotOptERotamerData method) (pyrosetta.rosetta.protocols.optimize_weights.SingleStructureData method) free_dof (pyrosetta.rosetta.core.scoring.ScoreType attribute) free_dof_options() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) free_res (pyrosetta.rosetta.core.scoring.ScoreType attribute) free_residues() (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1 method) (pyrosetta.rosetta.protocols.recces.options.RECCES_Options method) free_rsd() (pyrosetta.rosetta.protocols.recces.scratch.ThermalSamplingMover method) free_side_chain (pyrosetta.rosetta.core.scoring.ScoreType attribute) free_side_chain_bonus() (pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options method) free_sugar_bonus() (pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options method) free_suite (pyrosetta.rosetta.core.scoring.ScoreType attribute) free_suite_bonus() (pyrosetta.rosetta.core.scoring.methods.FreeDOF_Options method) FreeDOF_Energy (class in pyrosetta.rosetta.core.energy_methods) FreeDOF_EnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FreeDOF_Options (class in pyrosetta.rosetta.core.scoring.methods) FreePeptide (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover) FreePeptideMover (class in pyrosetta.rosetta.protocols.backbone_moves.local_backbone_mover.free_peptide_movers) freeze() (pyrosetta.rosetta.protocols.enzdes.PredesignPerturbMover 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.UniformSphereTransMover method) (pyrosetta.rosetta.protocols.topology_broker.RigidBodyRandomTMHMover method) freeze_sugar_torsions() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) freq() (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak3D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.CrossPeak4D.Spin method) (pyrosetta.rosetta.protocols.noesy_assign.FloatingResonance method) (pyrosetta.rosetta.protocols.noesy_assign.LabelResonance method) (pyrosetta.rosetta.protocols.noesy_assign.ProtonResonance method) (pyrosetta.rosetta.protocols.noesy_assign.Resonance method) frequencies (pyrosetta.rosetta.protocols.indexed_structure_store.SegmentSequenceProfileResult property) frequencies() (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase method) frequency() (pyrosetta.rosetta.core.scoring.nmr.NMRDummySpinlabelConformer method) (pyrosetta.rosetta.protocols.abinitio.PairingStatEntry method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequencies method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.AAFrequency method) (pyrosetta.rosetta.protocols.denovo_design.task_operations.ConsensusLoopDatabase method) frequency_in_taboo_map() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) fresh_instance() (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset 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.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.RunSimpleMetricsMover 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.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.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.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.RemoveConstraints 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.PeptideStubMover 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.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.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.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.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.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.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.SetAACompositionPotential method) (pyrosetta.rosetta.protocols.fldsgn.potentials.SetSecStructEnergies 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.FilterStructs method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat method) (pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge 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.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.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.genetic_algorithm.EntityElement 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.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.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.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.multistate_design.PosType 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.noesy_assign.PeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureDependentPeakCalibrator method) (pyrosetta.rosetta.protocols.noesy_assign.StructureIndependentPeakCalibrator 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_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.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.qsar.qsarMover method) (pyrosetta.rosetta.protocols.qsar.RenderGridsToKinemage method) (pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader 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.StoreResidueSubsetMover 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.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.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.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.STMStoredTask 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.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) frh (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) frh1 (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL property) frh2 (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL property) frh3 (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL property) frh4 (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL property) FRH_FRL (class in pyrosetta.rosetta.protocols.antibody.grafting) fringe_dDome_dBase() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) fringe_dDome_dOther() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) fringe_dDome_dWater() (pyrosetta.rosetta.core.scoring.lkball.DerivativeFinder method) frl (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Antibody_Database_Result property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_BlastResult property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_Results property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultSet property) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_SubstitutionMatrixResult property) frl1 (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL property) frl2 (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL property) frl3 (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL property) frl4 (pyrosetta.rosetta.protocols.antibody.grafting.FRH_FRL property) frob_distance() (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) from_array() (in module pyrosetta.bindings.homogeneous_transform) (pyrosetta.rosetta.numeric.HomogeneousTransform_Double class method) from_bond_cst() (pyrosetta.rosetta.core.kinematics.Jump method) from_chain() (pyrosetta.rosetta.protocols.indexed_structure_store.movers.DirectSegmentLookupMover method) from_entry() (pyrosetta.rosetta.protocols.protein_interface_design.PatchdockReader method) (pyrosetta.rosetta.protocols.splice.RBInMover method) from_euler_angles_deg() (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) from_euler_angles_rad() (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) from_four_points() (pyrosetta.rosetta.core.kinematics.Stub method) (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) from_other_chains() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) from_pose_datacache() (pyrosetta.rosetta.core.select.residue_selector.CachedResidueSubset static method) from_quaternion() (pyrosetta.rosetta.numeric.Py_xyzTransform_double method) (pyrosetta.rosetta.numeric.xyzTransform_double_t method) (pyrosetta.rosetta.numeric.xyzTransform_float_t method) from_remark() (pyrosetta.rosetta.protocols.fold_from_loops.movers.LabelPoseFromResidueSelectorMover method) from_res() (pyrosetta.rosetta.protocols.simple_filters.SSMotifFinder method) (pyrosetta.rosetta.protocols.simple_filters.StemFinder method) (pyrosetta.rosetta.protocols.splice.Splice method) from_RT() (in module pyrosetta.bindings.homogeneous_transform) (pyrosetta.rosetta.numeric.HomogeneousTransform_Double class method) from_same_chain() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) FROM_SCRATCH (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.MoveType attribute) from_scratch_frequency() (pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover.options.StepWiseMoveSelectorOptions method) (pyrosetta.rosetta.protocols.stepwise.monte_carlo.options.StepWiseMonteCarloOptions method) from_span() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) from_span_positive_z() (pyrosetta.rosetta.protocols.membrane.geometry.EmbeddingDef method) from_spans() (pyrosetta.rosetta.protocols.membrane.geometry.Embedding method) from_stubs() (pyrosetta.rosetta.core.kinematics.Jump method) (pyrosetta.rosetta.core.kinematics.RT method) from_subset() (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) FromScratchMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) FromScratchMoverCreator (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) front() (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.scoring.motif.MotifHits method) (pyrosetta.rosetta.core.scoring.motif.ResPairMotifs method) (pyrosetta.rosetta.core.select.residue_selector.ResidueRanges method) (pyrosetta.rosetta.core.select.residue_selector.ResidueVector method) (pyrosetta.rosetta.numeric.Xforms method) (pyrosetta.rosetta.protocols.antibody.grafting.SCS_ResultVector method) (pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases method) (pyrosetta.rosetta.protocols.denovo_design.components.EnumeratedVectorSelector_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution method) (pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions method) (pyrosetta.rosetta.protocols.denovo_design.components.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.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.legacy_sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.AAMatrix method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.monte_carlo.AcceptedScores method) (pyrosetta.rosetta.protocols.moves.CycleMover method) (pyrosetta.rosetta.protocols.moves.MoverContainer method) (pyrosetta.rosetta.protocols.moves.RandomMover method) (pyrosetta.rosetta.protocols.moves.SequenceMover method) (pyrosetta.rosetta.protocols.moves.SwitchMover method) (pyrosetta.rosetta.protocols.sewing.hashing.SegmentVector method) (pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints method) (pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t method) (pyrosetta.rosetta.std.list_const_protocols_match_Hit__star__t method) (pyrosetta.rosetta.std.list_core_id_AtomID_t method) (pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t method) (pyrosetta.rosetta.std.list_core_scoring_custom_pair_distance_atoms_and_func_struct_t method) (pyrosetta.rosetta.std.list_core_scoring_power_diagram_PDvertex__star__t method) (pyrosetta.rosetta.std.list_double_t method) (pyrosetta.rosetta.std.list_int_t method) (pyrosetta.rosetta.std.list_numeric_xyzVector_double_t method) (pyrosetta.rosetta.std.list_protocols_match_Hit_t method) (pyrosetta.rosetta.std.list_protocols_multistage_rosetta_scripts_mover_or_filter_t method) (pyrosetta.rosetta.std.list_protocols_pockets_spherical_coor_triplet_t method) (pyrosetta.rosetta.std.list_RDKit_Atom__star__t method) (pyrosetta.rosetta.std.list_RDKit_Bond__star__t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BasePair_t method) (pyrosetta.rosetta.std.list_std_pair_double_core_pose_rna_BaseStack_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_double_t method) (pyrosetta.rosetta.std.list_std_pair_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.std.list_std_set_std_string_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_chemical_ResidueType_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_operation_ResLvlTaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_chunk_library_inputters_ChunkLibraryInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_full_model_inputters_FullModelInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_inputters_PoseInputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_PoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_protocols_jd3_pose_outputters_SecondaryPoseOutputterCreator_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_Tag_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_const_utility_tag_XMLSchemaParticle_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_interaction_graph_AnnealableGraphBase_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_rotamer_set_RotamerOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_core_scoring_power_diagram_PDvertex_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_environment_claims_EnvClaim_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_deallocation_DeallocationMessage_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_LarvalJob_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_output_OutputSpecification_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_jd3_pose_outputters_SecondaryPoseOutputter_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamAlgorithm_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_match_downstream_DownstreamBuilder_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_CrossPeak_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_noesy_assign_PeakAssignment_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t method) (pyrosetta.rosetta.std.list_std_shared_ptr_utility_SimulateMPIMessage_t method) (pyrosetta.rosetta.std.list_std_string_t method) (pyrosetta.rosetta.std.list_unsigned_long_t method) (pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t method) (pyrosetta.rosetta.std.list_utility_tag_XMLSchemaSimpleSubelementList_ElementSummary_t method) (pyrosetta.rosetta.std.list_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.std.list_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.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) (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) 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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) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_power_diagram_SAnode_std_allocator_core_scoring_power_diagram_SAnode_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_rna_chemical_shift_ChemicalShiftData_std_allocator_core_scoring_rna_chemical_shift_ChemicalShiftData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_core_scoring_ScoreType_std_allocator_core_scoring_ScoreType_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_float_std_allocator_float_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_int_std_allocator_int_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_long_std_allocator_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_HomogeneousTransform_double_std_allocator_numeric_HomogeneousTransform_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_interpolation_spline_BicubicSpline_std_allocator_numeric_interpolation_spline_BicubicSpline_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_interpolation_spline_CubicSpline_std_allocator_numeric_interpolation_spline_CubicSpline_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_float_std_allocator_numeric_xyzVector_float_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_ObjexxFCL_ubyte_std_allocator_ObjexxFCL_ubyte_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_antibody_FrameWork_std_allocator_protocols_antibody_FrameWork_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_denovo_design_components_StrandOrientation_std_allocator_protocols_denovo_design_components_StrandOrientation_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_denovo_design_components_StructureSlice_std_allocator_protocols_denovo_design_components_StructureSlice_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_frag_picker_scores_GunnTuple_std_allocator_protocols_frag_picker_scores_GunnTuple_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_jd3_dag_node_managers_ResultElements_std_allocator_protocols_jd3_dag_node_managers_ResultElements_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_legacy_sewing_SewSegment_std_allocator_protocols_legacy_sewing_SewSegment_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_ligand_docking_ga_ligand_dock_PlaceableRotamer_std_allocator_protocols_ligand_docking_ga_ligand_dock_PlaceableRotamer_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_loops_Loops_std_allocator_protocols_loops_Loops_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_make_rot_lib_CentroidRotNum_std_allocator_protocols_make_rot_lib_CentroidRotNum_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_match_Hit_std_allocator_protocols_match_Hit_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_splice_ROT_std_allocator_protocols_splice_ROT_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_stepwise_legacy_modeler_rna_Cluster_Member_std_allocator_protocols_stepwise_legacy_modeler_rna_Cluster_Member_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_stepwise_modeler_protein_MainChainTorsionSet_std_allocator_protocols_stepwise_modeler_protein_MainChainTorsionSet_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_toolbox_match_enzdes_util_ExternalGeomSampler_std_allocator_protocols_toolbox_match_enzdes_util_ExternalGeomSampler_t method) (pyrosetta.rosetta.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__t method) (pyrosetta.rosetta.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__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_std_allocator_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_int_int_std_allocator_std_pair_int_int_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_std_allocator_std_pair_numeric_xyzVector_double_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_std_allocator_std_pair_std_shared_ptr_protocols_frag_picker_FragmentCandidate_std_shared_ptr_protocols_frag_picker_scores_FragmentScoreMap_t method) 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(pyrosetta.rosetta.utility.vector1_utility_vector1_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_std_allocator_std_set_protocols_match_upstream_hit_std_less_protocols_match_upstream_hit_std_allocator_protocols_match_upstream_hit_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_conformation_Residue_std_allocator_std_shared_ptr_const_core_conformation_Residue_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_std_allocator_std_shared_ptr_const_core_scoring_dna_TorsionFourierComponent_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_std_allocator_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_std_allocator_std_shared_ptr_const_protocols_match_upstream_ScaffoldBuildPoint_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_std_allocator_std_shared_ptr_const_protocols_simple_filters_ResidueDepthData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_conformation_Residue_std_allocator_std_shared_ptr_core_conformation_Residue_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_kinematics_tree_Atom_std_allocator_std_shared_ptr_core_kinematics_tree_Atom_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_optimization_DOF_Node_std_allocator_std_shared_ptr_core_optimization_DOF_Node_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_interaction_graph_NPDHBond_std_allocator_std_shared_ptr_core_pack_interaction_graph_NPDHBond_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_pack_task_ResfileCommand_std_allocator_std_shared_ptr_core_pack_task_ResfileCommand_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_scoring_saxs_DistanceHistogram_std_allocator_std_shared_ptr_core_scoring_saxs_DistanceHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_core_sequence_Cell_std_allocator_std_shared_ptr_core_sequence_Cell_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_antibody_PDBLandmark_std_allocator_std_shared_ptr_protocols_antibody_PDBLandmark_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_HelixPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_std_allocator_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_std_allocator_std_shared_ptr_protocols_flexpack_rotamer_set_FlexbbRotamerSet_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_std_allocator_std_shared_ptr_protocols_frag_picker_quota_QuotaPool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AdaptiveScoreHistogram_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_AtomPairConstraintsData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_std_allocator_std_shared_ptr_protocols_frag_picker_scores_FourAtomsConstraintData_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_Entity_std_allocator_std_shared_ptr_protocols_genetic_algorithm_Entity_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_genetic_algorithm_EntityElement_std_allocator_std_shared_ptr_protocols_genetic_algorithm_EntityElement_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_jd3_JGJobNode_std_allocator_std_shared_ptr_protocols_jd3_JGJobNode_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_std_allocator_std_shared_ptr_protocols_minimization_packing_MinimalRotamer_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_std_allocator_std_shared_ptr_protocols_pose_sewing_data_storage_SegmentEnvelope_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key2Tuple_unsigned_long_unsigned_long_std_allocator_utility_keys_Key2Tuple_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_std_allocator_utility_keys_Key3Tuple_unsigned_long_unsigned_long_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_std_allocator_utility_OrderedTuple_utility_fixedsizearray1_unsigned_long_2_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_std_allocator_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_core_scoring_nmr_VoxelGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint__star__const_numeric_xyzVector_double__star__t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_std_allocator_utility_vector1_std_pair_double_double_std_allocator_std_pair_double_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_std_allocator_utility_vector1_unsigned_long_std_allocator_unsigned_long_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_utility_vector1_bool_std_allocator_bool_std_allocator_utility_vector1_bool_std_allocator_bool_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_utility_vector1_double_std_allocator_double_std_allocator_utility_vector1_double_std_allocator_double_t method) (pyrosetta.rosetta.utility.vector1_utility_vector1_void__star__std_allocator_void__star__t method) fshave1 (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) fshave2 (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) fshave3 (pyrosetta.rosetta.protocols.mpi_refinement.MethodParams property) Fstring (class in pyrosetta.rosetta.ObjexxFCL) Fstring_of() (in module pyrosetta.rosetta.ObjexxFCL) Fsubstring (class in pyrosetta.rosetta.ObjexxFCL) ft_close_chains() (pyrosetta.rosetta.core.import_pose.options.RNA_DeNovoProtocolOptions method) (pyrosetta.rosetta.core.import_pose.options.RNA_FragmentMonteCarloOptions method) ft_mover() (pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover method) ftoa() (in module pyrosetta.rosetta.protocols.sparta) (pyrosetta.rosetta.protocols.sparta.ANN method) ftol (pyrosetta.rosetta.numeric.nls.lm_control_struct property) FTR_DONT_CARE (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) FTR_LOOPS_WITH_CUTS (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) FTR_SIMPLE_TREE (pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest attribute) Full (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) full_accuracy_when_scoring() (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.SapConstraintOptions method) full_align_res (pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo property) full_annotated_sequence() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) full_atom_beam() (pyrosetta.rosetta.protocols.loop_grower.LoopGrower method) FULL_ATOM_t (pyrosetta.rosetta.core.chemical.TypeSetMode attribute) full_block (pyrosetta.rosetta.core.pack.guidance_scoreterms.sap.BlockParam property) full_cache_name() (in module pyrosetta.rosetta.basic.database) full_definition() (pyrosetta.rosetta.utility.tag.XMLSchemaDefinition method) full_hit() (in module pyrosetta.rosetta.protocols.match) full_length_rmsd_over_residue_list() (in module pyrosetta.rosetta.protocols.stepwise.legacy.modeler.rna) full_model_from_input_source() (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.PDBFullModelInputter method) (pyrosetta.rosetta.protocols.jd3.full_model_inputters.SilentFileFullModelInputter method) FULL_MODEL_INFO (pyrosetta.rosetta.core.pose.datacache.CacheableDataType attribute) (pyrosetta.rosetta.core.pose.datacache.CacheableDataType.Enum attribute) full_model_info_defined() (in module pyrosetta.rosetta.core.pose.full_model_info) full_model_info_into_pose() (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) full_model_inputter (pyrosetta.rosetta.protocols.jd3.full_model.FullModelPreliminaryLarvalJob property) full_model_inputter_creators() (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory method) full_model_inputter_xml_schema_group_name() (pyrosetta.rosetta.protocols.jd3.full_model_inputters.FullModelInputterFactory static method) full_model_inputter_xsd_type_definition_w_attributes() (in module pyrosetta.rosetta.protocols.jd3.full_model_inputters) full_model_parameter_type_from_string() (in module pyrosetta.rosetta.core.pose.full_model_info) full_model_parameters() (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.core.pose.full_model_info.FullModelInfo method) full_model_pose_for_constraints() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) full_model_size() (in module pyrosetta.rosetta.core.pose.full_model_info) full_motif_score() (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyCalciumMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyInterModelMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyMotifScorer method) (pyrosetta.rosetta.protocols.legacy_sewing.scoring.LegacyPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.InterModelMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.IntraDesignTerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.MotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.PartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SegmentContactOrderScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.StartingNodeMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.SubsetPartnerMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TerminusMotifScorer method) (pyrosetta.rosetta.protocols.sewing.scoring.TopNMotifScorer method) FULL_NAME (pyrosetta.rosetta.core.simple_metrics.metrics.SequenceMetricMode attribute) full_name() (in module pyrosetta.rosetta.basic.database) (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfo method) full_name_from_aa() (in module pyrosetta.rosetta.core.chemical) full_sample_rot_index_2_moltenres_sample_rot_index() (pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets method) full_score_count (pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct property) full_sequence() (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) full_to_conventional() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) full_to_conventional_resnum_and_chain_and_segid() (pyrosetta.rosetta.core.pose.full_model_info.FullModelParameters method) full_to_sub() (in module pyrosetta.rosetta.core.pose.full_model_info) (pyrosetta.rosetta.core.pose.full_model_info.FullModelInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.protein.InputStreamWithResidueInfo method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseBasicWorkingParameters method) (pyrosetta.rosetta.protocols.stepwise.modeler.working_parameters.StepWiseWorkingParameters method) full_twobody_energy() (pyrosetta.rosetta.protocols.hbnet.NetworkState method) fullatom() (pyrosetta.rosetta.core.io.raw_data.DecoyStruct method) (pyrosetta.rosetta.core.io.silent.BinarySilentStruct method) (pyrosetta.rosetta.core.io.silent.RNA_SilentStruct method) fullatom_fast_relax_rounds() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) fullatom_filter() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) fullatom_find_disulfides() (pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions method) fullatom_mode_perturbation() (pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler method) fullatom_scorefunction() (pyrosetta.rosetta.protocols.forge.components.BDR method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelMover method) (pyrosetta.rosetta.protocols.splice.TailSegmentMover method) fullatom_scorefxn() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints 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.fold_from_loops.movers.NubInitioLoopClosureMover method) (pyrosetta.rosetta.protocols.fold_from_loops.NubInitioMover method) fullatom_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) FullatomCustomPairDistanceEnergy (class in pyrosetta.rosetta.core.scoring.custom_pair_distance) FullatomCustomPairDistanceEnergyCreator (class in pyrosetta.rosetta.core.scoring.custom_pair_distance) FullatomDisulfideEnergy (class in pyrosetta.rosetta.core.energy_methods) FullatomDisulfideEnergyComponents (class in pyrosetta.rosetta.core.scoring.disulfides) FullatomDisulfideEnergyContainer (class in pyrosetta.rosetta.core.scoring.disulfides) FullatomDisulfideEnergyCreator (class in pyrosetta.rosetta.core.energy_methods) FullatomDisulfideParams13 (class in pyrosetta.rosetta.core.scoring.disulfides) FullatomDisulfidePotential (class in pyrosetta.rosetta.core.scoring.disulfides) FullatomRelaxMover (class in pyrosetta.rosetta.protocols.surface_docking) FullAtomRNA_Fragments (class in pyrosetta.rosetta.core.fragment.rna) FullChiSampleSet (class in pyrosetta.rosetta.protocols.match.upstream) FullModelInfo (class in pyrosetta.rosetta.core.pose.full_model_info) FullModelInnerLarvalJob (class in pyrosetta.rosetta.protocols.jd3.full_model) FullModelInputSource (class in pyrosetta.rosetta.protocols.jd3.full_model_inputters) FullModelInputter (class in pyrosetta.rosetta.protocols.jd3.full_model_inputters) FullModelInputterCreator (class in pyrosetta.rosetta.protocols.jd3.full_model_inputters) FullModelInputterFactory (class in pyrosetta.rosetta.protocols.jd3.full_model_inputters) FullModelJobQueen (class in pyrosetta.rosetta.protocols.jd3.full_model) FullModelParameters (class in pyrosetta.rosetta.core.pose.full_model_info) FullModelParameterType (class in pyrosetta.rosetta.core.pose.full_model_info) FullModelPoseBuilder (class in pyrosetta.rosetta.core.import_pose) FullModelPreliminaryLarvalJob (class in pyrosetta.rosetta.protocols.jd3.full_model) fullname() (pyrosetta.rosetta.core.io.nmr.SpinlabelDatabaseEntry method) fully_counted() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) fully_excluded_1b() (pyrosetta.rosetta.core.scoring.ResidueExclParams method) Func (class in pyrosetta.rosetta.core.scoring.func) FUNC (pyrosetta.rosetta.basic.ProfTag attribute) func() (pyrosetta.rosetta.core.scoring.CenHBPotential method) (pyrosetta.rosetta.core.scoring.constraints.AngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.BoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.DOF_Constraint method) (pyrosetta.rosetta.core.scoring.constraints.NamedAngleConstraint method) (pyrosetta.rosetta.core.scoring.constraints.OffsetPeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.constraints.PeriodicBoundFunc method) (pyrosetta.rosetta.core.scoring.custom_pair_distance.DistanceFunc method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCb_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CaCbCbCa_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CB_Angle_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cb_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.CBSG_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.Cen_Distance_Func method) (pyrosetta.rosetta.core.scoring.disulfides.NCaCaC_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.disulfides.SG_Dist_Func method) (pyrosetta.rosetta.core.scoring.disulfides.SGSG_Dihedral_Func method) (pyrosetta.rosetta.core.scoring.func.AmberPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CharmmPeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularGeneral1D_Func method) (pyrosetta.rosetta.core.scoring.func.CircularHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.CircularPowerFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSigmoidalFunc method) (pyrosetta.rosetta.core.scoring.func.CircularSplineFunc method) (pyrosetta.rosetta.core.scoring.func.ConstantFunc method) (pyrosetta.rosetta.core.scoring.func.CountViolFunc method) (pyrosetta.rosetta.core.scoring.func.EtableFunc method) (pyrosetta.rosetta.core.scoring.func.FadeFunc method) (pyrosetta.rosetta.core.scoring.func.FlatHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.Func method) (pyrosetta.rosetta.core.scoring.func.GaussianChainDoubleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainGeneralFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainQuadrupleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainSingleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianChainTripleFunc method) (pyrosetta.rosetta.core.scoring.func.GaussianFunc method) (pyrosetta.rosetta.core.scoring.func.HarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.IdentityFunc method) (pyrosetta.rosetta.core.scoring.func.KarplusFunc method) (pyrosetta.rosetta.core.scoring.func.LinearPenaltyFunction method) (pyrosetta.rosetta.core.scoring.func.MinMultiHarmonicFunc method) (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) (pyrosetta.rosetta.core.scoring.func.PeriodicFunc method) (pyrosetta.rosetta.core.scoring.func.ScalarWeightedFunc method) (pyrosetta.rosetta.core.scoring.func.SigmoidFunc method) (pyrosetta.rosetta.core.scoring.func.SkipViolFunc method) (pyrosetta.rosetta.core.scoring.func.SmoothStepFunc method) (pyrosetta.rosetta.core.scoring.func.SoedingFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc method) (pyrosetta.rosetta.core.scoring.func.SOGFunc_Impl method) (pyrosetta.rosetta.core.scoring.func.SplineFunc method) (pyrosetta.rosetta.core.scoring.func.SquareWell2Func method) (pyrosetta.rosetta.core.scoring.func.SquareWellFunc method) (pyrosetta.rosetta.core.scoring.func.SumFunc method) (pyrosetta.rosetta.core.scoring.func.TopOutFunc method) (pyrosetta.rosetta.core.scoring.func.USOGFunc method) (pyrosetta.rosetta.core.scoring.SmoothScoreTermCoeffs method) (pyrosetta.rosetta.protocols.jumping.ChainbreakDistFunc method) (pyrosetta.rosetta.protocols.moves.FastLinearFunc method) (pyrosetta.rosetta.protocols.moves.GeometricFunc method) (pyrosetta.rosetta.protocols.moves.InvGeometricFunc method) (pyrosetta.rosetta.protocols.moves.LinearFunc method) (pyrosetta.rosetta.protocols.moves.RampingFunc method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix method) (pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd method) func_ (pyrosetta.rosetta.core.scoring.custom_pair_distance.atoms_and_func_struct property) (pyrosetta.rosetta.core.scoring.custom_pair_distance.resatom_and_func_struct property) func_() (pyrosetta.rosetta.core.scoring.func.MixtureFunc method) func_1d (class in pyrosetta.rosetta.core.optimization) func_groups() (pyrosetta.rosetta.protocols.relax.AtomCoordinateCstMover method) func_soft() (pyrosetta.rosetta.core.scoring.CenHBPotential method) FuncFactory (class in pyrosetta.rosetta.core.scoring.func) funcs() (pyrosetta.rosetta.core.scoring.func.SumFunc method) FUNCTION (pyrosetta.rosetta.numeric.expression_parser.TokenType attribute) function() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTFunction method) function_expression() (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunction method) (pyrosetta.rosetta.protocols.pack_daemon.DynamicAggregateFunctionDriver method) (pyrosetta.rosetta.protocols.pack_daemon.EntityFunc method) function_tag() (pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.GeomSampleInfo method) FunctionToken (class in pyrosetta.rosetta.numeric.expression_parser) FunGroupTK (class in pyrosetta.rosetta.protocols.kinmatch) FURANOSE (pyrosetta.rosetta.core.chemical.ResidueProperty attribute) Fv (pyrosetta.rosetta.protocols.antibody_legacy.Antibody property) Fv_sequence_ (pyrosetta.rosetta.protocols.antibody_legacy.Antibody property) fw_all (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.jacobian_struct property) fw_cons (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.jacobian_struct property) fw_dofs (pyrosetta.rosetta.core.kinematics.jacobian.ModuleType1.jacobian_struct property)