Index – B

B() (pyrosetta.rosetta.core.scoring.electron_density.OneGaussianScattering method) b1() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) b1_b2_Ktheta() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) b1_b2_theta0() (pyrosetta.rosetta.protocols.branch_angle.BranchParam2 method) b1_bond_angle_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_bond_angle_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_bond_angle_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_torsion_offset_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_torsion_offset_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b1_torsion_offset_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef1 method) (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) b2_bond_angle_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_bond_angle_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_bond_angle_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_torsion_offset_A() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_torsion_offset_B() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) b2_torsion_offset_C() (pyrosetta.rosetta.protocols.branch_angle.BranchCoef2 method) bab_motif() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) bab_motifs() (pyrosetta.rosetta.protocols.fldsgn.topology.BetaAlphaBetaMotifSet method) back() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidues method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSections method) (pyrosetta.rosetta.protocols.jd2.JobsContainer method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.ligand_docking.ligand_options.Interface method) (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) (pyrosetta.rosetta.protocols.sewing.SegmentGraph method) (pyrosetta.rosetta.protocols.simple_moves.AcceptedScores method) backbone() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) backbone_aa() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) backbone_backbone_energy() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) backbone_burial() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) backbone_exposed() (pyrosetta.rosetta.core.pose.rna.RNA_DataInfo method) backbone_mover_complex_type_namer() (pyrosetta.rosetta.protocols.simple_moves.BackboneMover method) (pyrosetta.rosetta.protocols.simple_moves.ShearMover method) (pyrosetta.rosetta.protocols.simple_moves.SmallMover method) backbone_only() (pyrosetta.rosetta.protocols.match.upstream.BuildSet method) backbone_sidechain_energy() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) backbone_stub_match() (in module pyrosetta.rosetta.protocols.motifs) BackboneGridSamplerHelper (class in pyrosetta.rosetta.protocols.helical_bundle) BackboneMover (class in pyrosetta.rosetta.protocols.simple_moves) BackboneStubConstraint (class in pyrosetta.rosetta.core.scoring.constraints) BackboneStubLinearConstraint (class in pyrosetta.rosetta.core.scoring.constraints) backrub_cdrs() (pyrosetta.rosetta.protocols.antibody.design.GeneralAntibodyModeler method) backrub_rotation_angles() (in module pyrosetta.rosetta.protocols.backrub) backrub_rotation_constants() (in module pyrosetta.rosetta.protocols.backrub) BackrubMover (class in pyrosetta.rosetta.protocols.backrub) BackrubSegment (class in pyrosetta.rosetta.protocols.backrub) bad() (pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob method) (pyrosetta.rosetta.protocols.jd2.InnerJob method) (pyrosetta.rosetta.protocols.jd2.Job method) (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) BalancedKicMover (class in pyrosetta.rosetta.protocols.kinematic_closure) BANGLE_MIN() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) BANGLE_SD() (pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure.KinematicMover method) bare_name() (pyrosetta.rosetta.utility.file.FileName method) Base (class in pyrosetta.rosetta.utility.py) base() (pyrosetta.rosetta.utility.file.FileName method) base5index2symbolString() (pyrosetta.rosetta.core.sequence.ABEGOManager method) base_atoms_square_deviation() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) base_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_backbone_distance_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) base_backbone_rho_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) base_backbone_z_cutoff() (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) base_centroids() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) base_geometry_height_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_geometry_orientation_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_name() (in module pyrosetta.rosetta.protocols.vip) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_CS_residue_parameters method) base_native_bonus() (pyrosetta.rosetta.protocols.sewing.AssemblyConstraintsMover method) base_pair_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_pair_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) base_pair_moving() (in module pyrosetta.rosetta.protocols.rna.denovo) base_pair_step_moving() (in module pyrosetta.rosetta.protocols.rna.denovo) base_residue_types() (pyrosetta.rosetta.core.chemical.GlobalResidueTypeSet method) (pyrosetta.rosetta.core.chemical.PoseResidueTypeSet method) (pyrosetta.rosetta.core.chemical.ResidueTypeSet method) base_stack_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_stack_axis_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_stack_list() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) base_stagger_array() (pyrosetta.rosetta.core.pose.rna.RNA_RawBaseBaseInfo method) base_stubs() (pyrosetta.rosetta.core.scoring.rna.RNA_CentroidInfo method) base_type() (pyrosetta.rosetta.utility.tag.XMLSchemaRestriction method) BaseArchiveManager (class in pyrosetta.rosetta.protocols.jd2.archive) BaseJobDistributor (class in pyrosetta.rosetta.protocols.jobdist) BaseJumpSetup (class in pyrosetta.rosetta.protocols.jumping) baseline_checkpointing_filename() (pyrosetta.rosetta.protocols.simple_filters.Sigmoid method) basepair_axis_stagger_scaling() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) BasePairConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) BasePairStep (class in pyrosetta.rosetta.protocols.rna.denovo.base_pairs) BasePairStepLibrary (class in pyrosetta.rosetta.protocols.rna.denovo.libraries) BasePairStepSequence (class in pyrosetta.rosetta.protocols.rna.denovo.libraries) BasePairType (class in pyrosetta.rosetta.protocols.rna.denovo.libraries) BasePartner (class in pyrosetta.rosetta.core.scoring.dna) basestack_axis_scaling() (pyrosetta.rosetta.core.pose.rna.RNA_FilteredBaseBaseInfo method) BaseTabooPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) basic_idealize() (in module pyrosetta.rosetta.protocols.idealize) BasicCDRClusterSet (class in pyrosetta.rosetta.protocols.antibody.clusters) BasicDataCache (class in pyrosetta.rosetta.basic.datacache) BasicJob (class in pyrosetta.rosetta.protocols.jobdist) Basis (class in pyrosetta.rosetta.protocols.sewing) basis_pair() (pyrosetta.rosetta.protocols.sewing.HashEdge method) Batch (class in pyrosetta.rosetta.protocols.jd2.archive) batch() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) batch_get_xyz() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.pose.Pose method) batch_set_xyz() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.core.pose.Pose method) batches() (pyrosetta.rosetta.protocols.jd2.archive.ArchiveManager method) (pyrosetta.rosetta.protocols.jd2.archive.BaseArchiveManager method) BatchJobInputter (class in pyrosetta.rosetta.protocols.jd2) bb() (pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover method) (pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover method) bb_bb() (pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter method) bb_boltz_probs() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) bb_boltz_probs_per_aa() (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) bb_independent_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) bb_pair_score() (pyrosetta.rosetta.core.scoring.dssp.Dssp method) BB_Pos (class in pyrosetta.rosetta.core.scoring) (class in pyrosetta.rosetta.protocols.fldsgn.topology) bb_pos() (pyrosetta.rosetta.core.scoring.SS_Info method) (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) bb_rmsd() (in module pyrosetta.rosetta.core.scoring) bb_rmsd_including_O() (in module pyrosetta.rosetta.core.scoring) bbdep_bond_devs() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) bbdep_bond_params() (pyrosetta.rosetta.core.scoring.methods.IdealParametersDatabase method) BBDihedralSampler (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) BBDihedralSamplerBase (class in pyrosetta.rosetta.protocols.simple_moves.bb_sampler) BBDihedralSamplerMover (class in pyrosetta.rosetta.protocols.simple_moves) BBG8T3AMover (class in pyrosetta.rosetta.protocols.simple_moves) BBGaussianMover (class in pyrosetta.rosetta.protocols.simple_moves) bbnbrs() (pyrosetta.rosetta.protocols.evolution.NucleotideMutation method) bbpos_is_set() (pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2 method) bbtorsion_srfd() (pyrosetta.rosetta.core.fragment.picking_old.vall.VallResidue method) (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) be_lenient() (pyrosetta.rosetta.protocols.kinematic_closure.solution_pickers.FilteredSolutions method) been_accessed() (pyrosetta.rosetta.utility.options.BooleanOption method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.Option method) (pyrosetta.rosetta.utility.options.PathOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.ScalarOption method) (pyrosetta.rosetta.utility.options.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) (pyrosetta.rosetta.utility.options.VectorOption method) begin() (pyrosetta.rosetta.core.fragment.ConstantLengthFragSet method) (pyrosetta.rosetta.core.fragment.FragSet method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallLibrary method) (pyrosetta.rosetta.core.fragment.picking_old.vall.VallSection method) (pyrosetta.rosetta.core.io.raw_data.RawFileData method) (pyrosetta.rosetta.core.io.silent.SilentFileData method) (pyrosetta.rosetta.core.kinematics.FoldTree method) (pyrosetta.rosetta.core.optimization.symmetry.SymMinimizerMap method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.task.TaskFactory method) (pyrosetta.rosetta.core.scoring.EMapVector method) (pyrosetta.rosetta.core.scoring.constraints.ResidueConstraints method) (pyrosetta.rosetta.core.scoring.dssp.StrandPairingSet method) (pyrosetta.rosetta.numeric.kdtree.KDPointList method) (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) (pyrosetta.rosetta.protocols.fldsgn.topology.Loop method) (pyrosetta.rosetta.protocols.fldsgn.topology.Strand method) (pyrosetta.rosetta.protocols.fldsgn.topology.StrandPairingSet method) (pyrosetta.rosetta.protocols.forge.build.BuildManager method) (pyrosetta.rosetta.protocols.jumping.JumpSelector method) (pyrosetta.rosetta.protocols.jumping.JumpSetup method) (pyrosetta.rosetta.protocols.jumping.ResiduePairJumpSetup method) (pyrosetta.rosetta.protocols.kinematic_closure.ChainedSolutionList method) (pyrosetta.rosetta.protocols.loops.Loops method) (pyrosetta.rosetta.protocols.noesy_assign.ResonanceList method) (pyrosetta.rosetta.utility.graph.DirectedEdgeList method) (pyrosetta.rosetta.utility.graph.EdgeList method) (pyrosetta.rosetta.utility.options.BooleanVectorOption method) (pyrosetta.rosetta.utility.options.FileVectorOption method) (pyrosetta.rosetta.utility.options.IntegerVectorOption method) (pyrosetta.rosetta.utility.options.PathVectorOption method) (pyrosetta.rosetta.utility.options.RealVectorOption method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) begin1() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) begin_const() (pyrosetta.rosetta.core.io.raw_data.RawFileData method) begin_critical_section() (pyrosetta.rosetta.protocols.jobdist.AtomTreeDiffJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.BaseJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainPdbJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainRawJobDistributor method) (pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor method) begin_receptor_partner_pair() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) begin_structure() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverBasicStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverMarkdownStreamOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputter method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverOutputterContainer method) (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverPoseOutputter method) being_designed() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) being_packed() (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) (pyrosetta.rosetta.core.pack.task.ResidueLevelTask_ method) (pyrosetta.rosetta.core.scoring.FACTSPoseInfo method) (pyrosetta.rosetta.core.scoring.GenBornPoseInfo method) (pyrosetta.rosetta.core.scoring.MultipoleElecPoseInfo method) (pyrosetta.rosetta.core.scoring.VdWTinkerPoseInfo method) bend() (pyrosetta.rosetta.protocols.fldsgn.topology.Helix method) bend_level() (pyrosetta.rosetta.protocols.fldsgn.filters.StrandCurvatureByLevels method) bessel_roots() (in module pyrosetta.rosetta.core.scoring.fiber_diffraction) best_bbcst_residues() (in module pyrosetta.rosetta.protocols.protein_interface_design) best_cutpoint() (in module pyrosetta.rosetta.protocols.protein_interface_design) best_rotamer_energy() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) BestHotspotCstMover (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BestTotalScoreSelector (class in pyrosetta.rosetta.protocols.frag_picker) beta() (pyrosetta.rosetta.core.pose.Pose method) (pyrosetta.rosetta.core.scoring.CSA method) beta_aform() (pyrosetta.rosetta.core.chemical.rna.RNA_FittedTorsionInfo method) BetaAlphaBetaMotifSet (class in pyrosetta.rosetta.protocols.fldsgn.topology) BetaSheetArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) BetaTurnDetectionFeaturesCreator (class in pyrosetta.rosetta.protocols.features) bF() (pyrosetta.rosetta.protocols.frag_picker.VallResidue method) BFactor (class in pyrosetta.rosetta.protocols.frag_picker.scores) bfactor() (pyrosetta.rosetta.core.pose.PDBInfo method) BfactorFittingMover (class in pyrosetta.rosetta.protocols.electron_density) BfactorMPM (class in pyrosetta.rosetta.protocols.match) BfactorMultifunc (class in pyrosetta.rosetta.protocols.electron_density) Bi() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) BiasedFragmentMover (class in pyrosetta.rosetta.protocols.nonlocal) bIdealLoopClosing() (pyrosetta.rosetta.protocols.loops.loop_closure.ccd.WidthFirstSlidingWindowLoopClosure method) bigbin() (pyrosetta.rosetta.protocols.frags.VallData method) BigBinConstraint (class in pyrosetta.rosetta.core.scoring.constraints) BigBinConstraintCreator (class in pyrosetta.rosetta.core.scoring.constraints) bin() (pyrosetta.rosetta.core.scoring.constraints.BigBinConstraint method) (pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber method) bin6() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_center_point() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_from_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bin_index_hasher (class in pyrosetta.rosetta.numeric.geometry.hashing) bin_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) bin_params_file_name() (pyrosetta.rosetta.core.select.residue_selector.BinSelector method) bin_widths() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) BinarySilentStructCreator (class in pyrosetta.rosetta.core.io.silent) bind_method() (in module pyrosetta.util) BindingSiteConstraintCreator (class in pyrosetta.rosetta.protocols.constraints_additional) binname() (pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter method)

binner() (pyrosetta.rosetta.protocols.match.HitHasher method) BinSelector (class in pyrosetta.rosetta.core.select.residue_selector) bit_is_set() (in module pyrosetta.rosetta.core.pack.dunbrack) bit_or() (in module pyrosetta.rosetta.ObjexxFCL.bit) bite() (in module pyrosetta.rosetta.ObjexxFCL.format) blank() (in module pyrosetta.rosetta.ObjexxFCL) blank_atom_id_domain_map() (in module pyrosetta.rosetta.core.pose.copydofs) blanket_assign_state_0() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) BlankMatrixMult() (in module pyrosetta.rosetta.numeric.model_quality) block() (pyrosetta.rosetta.protocols.jd2.SingleFileBuffer method) (pyrosetta.rosetta.utility.signals.Link method) block_allocation_error_message() (in module pyrosetta.rosetta.utility.graph) block_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) blocked() (pyrosetta.rosetta.utility.signals.Link method) blocking_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) BlueprintArchitect (class in pyrosetta.rosetta.protocols.denovo_design.architects) boltz_rank() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) boltzmann() (pyrosetta.rosetta.protocols.moves.DualMonteCarlo method) (pyrosetta.rosetta.protocols.moves.MonteCarlo method) (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) boltzmann_accept_probability() (in module pyrosetta.rosetta.numeric) boltzmann_result() (pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer method) Bond (class in pyrosetta.rosetta.core.chemical) bond() (pyrosetta.rosetta.core.chemical.ResidueType method) bond_angle() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) bond_angle_central_atoms_to_score() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) bond_angle_dof_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) bond_angle_residue_type_param_set() (pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions method) bond_length() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) (pyrosetta.rosetta.core.kinematics.AtomTree method) (pyrosetta.rosetta.protocols.simple_moves.CutChainMover method) bond_length_dof_id() (pyrosetta.rosetta.core.kinematics.AtomTree method) bond_name() (pyrosetta.rosetta.core.chemical.Bond method) bondangle() (in module pyrosetta.rosetta.numeric.kinematic_closure) (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) (pyrosetta.rosetta.core.chemical.ResidueType method) BondAnglePerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) bondangles_for_atom() (pyrosetta.rosetta.core.chemical.ResidueType method) BondAromaticity (class in pyrosetta.rosetta.core.chemical) BondConjugability (class in pyrosetta.rosetta.core.chemical) bonded_neighbor() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) bonded_neighbor_all_res() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) bonded_orbitals() (pyrosetta.rosetta.core.chemical.Atom method) (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.conformation.Residue method) BondedAtom (class in pyrosetta.rosetta.core.kinematics.tree) BondedResidueSelector (class in pyrosetta.rosetta.core.select.residue_selector) BondID (class in pyrosetta.rosetta.core.id) bonding_distance_threshold() (in module pyrosetta.rosetta.core.io.pose_from_sfr) BooleanOption (class in pyrosetta.rosetta.utility.options) BooleanOptionKey (class in pyrosetta.rosetta.utility.options) BooleanVectorOption (class in pyrosetta.rosetta.utility.options) BooleanVectorOptionKey (class in pyrosetta.rosetta.utility.options) bools_from_sizes() (in module pyrosetta.rosetta.protocols.motifs) boost_closure_cycles() (pyrosetta.rosetta.protocols.forge.remodel.RemodelLoopMover method) bootstrapCATrace() (pyrosetta.rosetta.protocols.rbsegment_relax.FragInsertAndAlignMover method) born_radius() (pyrosetta.rosetta.core.scoring.GenBornResidueInfo method) bound_struct() (pyrosetta.rosetta.protocols.optimize_weights.DGBindOptEData method) boundary_left() (pyrosetta.rosetta.core.kinematics.FoldTree method) boundary_right() (pyrosetta.rosetta.core.kinematics.FoldTree method) bounded() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) bounded_loops_from_alignment() (in module pyrosetta.rosetta.protocols.comparative_modeling) bounded_protocol() (pyrosetta.rosetta.protocols.frag_picker.FragmentPicker method) bounded_value() (pyrosetta.rosetta.ObjexxFCL.DynamicIndexRange method) (pyrosetta.rosetta.ObjexxFCL.IndexRange method) (pyrosetta.rosetta.ObjexxFCL.StaticIndexRange method) bounding_box() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bounding_volume_from_index() (pyrosetta.rosetta.numeric.geometry.hashing.SixDCoordinateBinner method) bpdefs2map() (in module pyrosetta.rosetta.protocols.motifs) bQuickTest() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.FragmentSampler method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) BR() (pyrosetta.rosetta.core.scoring.FACTSResidueInfo method) branch_connect_atom_names() (pyrosetta.rosetta.core.chemical.ResidueType method) branch_connect_atoms() (pyrosetta.rosetta.core.chemical.ResidueType method) branch_variant_type_from_atom_name() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) branch_variant_type_from_position() (pyrosetta.rosetta.core.chemical.carbohydrates.CarbohydrateInfoManager method) BranchCoef1 (class in pyrosetta.rosetta.protocols.branch_angle) BranchCoef2 (class in pyrosetta.rosetta.protocols.branch_angle) BranchEnergy (class in pyrosetta.rosetta.core.scoring.methods) branching_atomid1() (in module pyrosetta.rosetta.protocols.branch_angle) branching_atomids2() (in module pyrosetta.rosetta.protocols.branch_angle) branchopt() (pyrosetta.rosetta.protocols.backrub.BackrubMover method) BranchParam1 (class in pyrosetta.rosetta.protocols.branch_angle) BranchParam2 (class in pyrosetta.rosetta.protocols.branch_angle) break_disulfide() (in module pyrosetta.rosetta.core.conformation) BRENT() (pyrosetta.rosetta.core.optimization.BrentLineMinimization method) BrentLineMinimization (class in pyrosetta.rosetta.core.optimization) Bridge (class in pyrosetta.rosetta.protocols.forge.build) bridge_objects() (in module pyrosetta.rosetta.numeric.kinematic_closure.radians) bridge_res() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) BridgeChainsMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) bridgeObjects() (in module pyrosetta.rosetta.numeric.kinematic_closure) bridgeObjects_nonredundant() (in module pyrosetta.rosetta.numeric.kinematic_closure) broker() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) broker_file() (pyrosetta.rosetta.protocols.jd2.archive.Batch method) Broker_main() (in module pyrosetta.rosetta.protocols.abinitio) brute_move_large() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) brute_move_small() (pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio method) (pyrosetta.rosetta.protocols.abinitio.FoldConstraints method) (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) brute_move_small_top25() (pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio method) BT_PROPERTIES (class in pyrosetta.rosetta.core.scoring.bin_transitions) BTSB_SUBBIN_TYPE (class in pyrosetta.rosetta.core.scoring.bin_transitions) buf() (pyrosetta.rosetta.basic.PyTracer method) buffer_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) buffer_size() (pyrosetta.rosetta.utility.io.ozstream method) buffering_signals() (pyrosetta.rosetta.core.conformation.Conformation method) (pyrosetta.rosetta.core.conformation.symmetry.MirrorSymmetricConformation method) (pyrosetta.rosetta.core.conformation.symmetry.SymmetricConformation method) build() (pyrosetta.rosetta.core.chemical.AtomICoor method) (pyrosetta.rosetta.core.scoring.lkball.WaterBuilder method) (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) build_anchorless_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_and_discard_first_round_hits_at_all_positions() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) build_atom_ideal() (pyrosetta.rosetta.core.conformation.Residue method) build_base_rotamers() (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) build_centroid_loop() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) build_chemical_edge() (in module pyrosetta.rosetta.core.conformation) build_dependent_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) build_dependent_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_dna_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_fake_xyz() (pyrosetta.rosetta.core.kinematics.Stub method) build_fold_tree() (pyrosetta.rosetta.protocols.topology_broker.DisulfJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.FragmentJumpClaimer method) (pyrosetta.rosetta.protocols.topology_broker.RigidChunkClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateFragmentClaimer method) (pyrosetta.rosetta.protocols.topology_broker.TemplateJumpClaimer method) build_from_three_coords() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) build_full_model() (in module pyrosetta.rosetta.protocols.stepwise.monte_carlo) build_fullatom_loop() (pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler method) build_helix() (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) build_hits_at_all_positions() (pyrosetta.rosetta.protocols.match.downstream.ClassicMatchAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.DownstreamAlgorithm method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToDownstreamResidue method) (pyrosetta.rosetta.protocols.match.downstream.SecondaryMatcherToUpstreamResidue method) build_independent_water_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_init_pose() (pyrosetta.rosetta.protocols.rna.movers.RNA_HelixAssembler method) build_jump_edge() (in module pyrosetta.rosetta.core.conformation) build_orbital_xyz() (pyrosetta.rosetta.core.conformation.Residue method) build_point() (pyrosetta.rosetta.protocols.match.Matcher method) build_polymer_edge() (in module pyrosetta.rosetta.core.conformation) build_pose() (in module pyrosetta.rosetta.core.import_pose) (pyrosetta.rosetta.core.io.pose_from_sfr.PoseFromSFRBuilder method) build_pose_as_is() (in module pyrosetta.rosetta.core.import_pose) build_pose_as_is2() (in module pyrosetta.rosetta.core.import_pose) build_pose_from_pdb_as_is() (in module pyrosetta.rosetta.core.io.pdb) build_random_dna_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_receptor_peptide_pose() (pyrosetta.rosetta.protocols.peptide_deriver.PeptideDeriverFilter method) build_residue_tree() (in module pyrosetta.rosetta.core.conformation) build_rna_rotamers() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_rot_matrix() (pyrosetta.rosetta.protocols.mean_field.RotMatrix method) build_rot_matrix_for_pose() (pyrosetta.rosetta.protocols.mean_field.DesignMeanField method) (pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField method) (pyrosetta.rosetta.protocols.mean_field.MeanField method) build_rotamer_list() (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.JumpRotamerSidechainMover method) (pyrosetta.rosetta.protocols.simple_moves.sidechain_moves.PerturbRotamerSidechainMover method) build_rotamers() (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) build_rotamers_from_rotamer_bins() (in module pyrosetta.rosetta.core.pack.rotamer_set) build_rotamers_lite() (in module pyrosetta.rosetta.protocols.motifs) build_stage() (pyrosetta.rosetta.protocols.loop_modeler.LoopModeler method) build_tree() (in module pyrosetta.rosetta.core.conformation) buildable() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) BuildAlaPose (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) BuildDeNovoBackboneMover (class in pyrosetta.rosetta.protocols.denovo_design.movers) BuildInstruction (class in pyrosetta.rosetta.protocols.forge.build) BuildManager (class in pyrosetta.rosetta.protocols.forge.build) BuildSet (class in pyrosetta.rosetta.protocols.match.upstream) buildsturm() (in module pyrosetta.rosetta.numeric.kinematic_closure) built_atom_vertex() (pyrosetta.rosetta.core.chemical.AtomICoor method) bulge_keyname() (pyrosetta.rosetta.protocols.denovo_design.architects.StrandArchitect method) bump_check() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamer_set.symmetry.SymmetricRotamerSet_ method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) (pyrosetta.rosetta.core.pack.task.PackerTask method) (pyrosetta.rosetta.core.pack.task.PackerTask_ method) bump_check_backbone() (pyrosetta.rosetta.core.scoring.ScoreFunction method) bump_check_full() (pyrosetta.rosetta.core.scoring.ScoreFunction method) bump_energy_backbone() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) bump_energy_full() (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) bump_filter() (pyrosetta.rosetta.core.pack.dunbrack.cenrot.SingleResidueCenrotLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleBasicRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleLigandRotamerLibrary method) (pyrosetta.rosetta.core.pack.rotamers.SingleResidueRotamerLibrary method) bump_grid() (pyrosetta.rosetta.protocols.match.output.UpstreamCollisionFilter method) (pyrosetta.rosetta.protocols.match.output.UpstreamDownstreamCollisionFilter method) bump_grid_to_enclose_pose() (in module pyrosetta.rosetta.protocols.match) bump_grid_to_enclose_residue() (in module pyrosetta.rosetta.protocols.match) bump_grid_to_enclose_residue_backbone() (in module pyrosetta.rosetta.protocols.match) bundle_symmetry() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) bundle_symmetry_copies() (pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet method) BundleGridSamplerHelper (class in pyrosetta.rosetta.protocols.helical_bundle) BundleParameters (class in pyrosetta.rosetta.protocols.helical_bundle.parameters) BundleParametersSet (class in pyrosetta.rosetta.protocols.helical_bundle.parameters) BundleReporterFilterBehaviour (class in pyrosetta.rosetta.protocols.helical_bundle) BuriedSurfaceAreaFilter (class in pyrosetta.rosetta.protocols.simple_filters) BuriedUnsatHbondFilter (class in pyrosetta.rosetta.protocols.simple_filters) byte (class in pyrosetta.rosetta.ObjexxFCL)