Index – V

v_begin() (pyrosetta.rosetta.protocols.loops.Loops method) v_end() (pyrosetta.rosetta.protocols.loops.Loops method) valence_electrons_p() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valence_electrons_s() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valence_electrons_sp() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valence_electrons_spd() (pyrosetta.rosetta.core.chemical.ElectronConfiguration method) valid() (pyrosetta.rosetta.core.id.AtomID method) (pyrosetta.rosetta.core.id.DOF_ID method) (pyrosetta.rosetta.core.id.JumpID method) (pyrosetta.rosetta.core.id.NamedAtomID method) (pyrosetta.rosetta.core.id.NamedStubID method) (pyrosetta.rosetta.core.id.StubID method) (pyrosetta.rosetta.core.id.TorsionID method) (pyrosetta.rosetta.core.kinematics.Edge method) (pyrosetta.rosetta.protocols.jd2.archive.Batch method) (pyrosetta.rosetta.protocols.nonlocal.Chunk method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator method) (pyrosetta.rosetta.utility.graph.EdgeListConstIterator method) (pyrosetta.rosetta.utility.graph.EdgeListIterator method) (pyrosetta.rosetta.utility.signals.Link method) valid_ends() (pyrosetta.rosetta.core.scoring.dssp.StrandPairing method) valid_names_string() (pyrosetta.rosetta.protocols.constraint_generator.ConstraintsMap method) valid_ss() (pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover method) (pyrosetta.rosetta.protocols.simple_moves.WobbleMover method) validate() (pyrosetta.rosetta.protocols.antibody.grafting.AntibodyChain method) validate_beta() (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) validate_dunbrack_binary() (pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary method) validate_input_script_against_xsd() (pyrosetta.rosetta.protocols.rosetta_scripts.RosettaScriptsParser method) validate_loop_start_stop() (in module pyrosetta.rosetta.protocols.loops) validate_talaris() (pyrosetta.rosetta.core.scoring.ScoreFunctionFactory method) validate_xml_against_xsd() (in module pyrosetta.rosetta.utility.tag) vall_key() (pyrosetta.rosetta.protocols.frag_picker.VallChunk method) vall_library_from_file() (in module pyrosetta.rosetta.core.fragment.picking_old.vall) vall_memory_usage() (pyrosetta.rosetta.protocols.forge.components.VarLengthBuild method) VallChunk (class in pyrosetta.rosetta.protocols.frag_picker) VallChunkFilter (class in pyrosetta.rosetta.protocols.frag_picker) vallChunksFromLibraries() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) vallChunksFromLibrary() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) VallData (class in pyrosetta.rosetta.protocols.frags) VallFragmentEval (class in pyrosetta.rosetta.core.fragment.picking_old.vall.eval) VallFragmentGen (class in pyrosetta.rosetta.core.fragment.picking_old.vall.gen) VallFragmentScore (class in pyrosetta.rosetta.core.fragment.picking_old.vall.scores) VallLibrarian (class in pyrosetta.rosetta.core.fragment.picking_old.vall) VallLibrary (class in pyrosetta.rosetta.core.fragment.picking_old.vall) vallNumLines() (pyrosetta.rosetta.protocols.frag_picker.VallProvider method) VallProvider (class in pyrosetta.rosetta.protocols.frag_picker) VallResidue (class in pyrosetta.rosetta.core.fragment.picking_old.vall) (class in pyrosetta.rosetta.protocols.frag_picker) VallResidues (class in pyrosetta.rosetta.core.fragment.picking_old.vall) VallSection (class in pyrosetta.rosetta.core.fragment.picking_old.vall) VallSections (class in pyrosetta.rosetta.core.fragment.picking_old.vall) Value (class in pyrosetta.rosetta.utility.py) value() (pyrosetta.rosetta.core.io.silent.SilentEnergy method) (pyrosetta.rosetta.ObjexxFCL.Dimension method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpression method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCon method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionCube method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionDiv method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMax method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMin method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionMul method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionPow method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionRef method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSquare method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSub method) (pyrosetta.rosetta.ObjexxFCL.DimensionExpressionSum method) (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) (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.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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) value_deriv() (pyrosetta.rosetta.core.scoring.hbonds.FadeInterval method) value_or() (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.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.StringOption method) (pyrosetta.rosetta.utility.options.StringVectorOption method) value_passes() (pyrosetta.rosetta.protocols.enzdes.ValueEvaluator method) value_set() (pyrosetta.rosetta.protocols.pack_daemon.InSetExpression method) value_string() (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) ValueEvaluator (class in pyrosetta.rosetta.protocols.enzdes) variable_name() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) variant_type_enums() (pyrosetta.rosetta.core.chemical.ResidueType method) variant_types() (pyrosetta.rosetta.core.chemical.ResidueType method) (pyrosetta.rosetta.core.pose.MiniPose method) variant_types_list() (pyrosetta.rosetta.core.pose.MiniPose method) variants_match() (in module pyrosetta.rosetta.core.chemical) variants_match_with_exceptions() (in module pyrosetta.rosetta.core.chemical) VariantType (class in pyrosetta.rosetta.core.chemical) VarLengthBuild (class in pyrosetta.rosetta.protocols.forge.components) vars_to_dofs() (pyrosetta.rosetta.protocols.ncbb.SecStructMinimizeMultiFunc method) (pyrosetta.rosetta.protocols.normalmode.NormalModeMultifunc method) vary_polar_hydrogen_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) vary_rna_bond_geometry() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) vary_stepsize() (pyrosetta.rosetta.protocols.docking.SlideIntoContact method) (pyrosetta.rosetta.protocols.rigid.RigidBodyTransMover method) VaryLoopLengthMover (class in pyrosetta.rosetta.protocols.stepwise.monte_carlo.mover) vdw_cached_rep_screen_info_is_setup() (in module pyrosetta.rosetta.protocols.scoring) vdw_calculation_annotated_sequence() (pyrosetta.rosetta.core.scoring.rna.RNA_ScoringInfo method) VDW_rep_alignment_RMSD_CUTOFF() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) VDW_rep_delete_matching_res() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) VDW_rep_screen_info() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) VDW_rep_screen_physical_pose_clash_dist_cutoff() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) vdw_type() (pyrosetta.rosetta.core.scoring.VdWTinkerResidueInfo method) VdWTinkerPoseInfo (class in pyrosetta.rosetta.core.scoring)

VdWTinkerPotential (class in pyrosetta.rosetta.core.scoring) VdWTinkerResidueInfo (class in pyrosetta.rosetta.core.scoring) VdWTinkerRotamerSetInfo (class in pyrosetta.rosetta.core.scoring) vec3_to_stub() (in module pyrosetta.rosetta.protocols.sic_dock) vec_distance() (in module pyrosetta.rosetta.numeric.kdtree) vector() (pyrosetta.rosetta.utility.options.AnyOptionKey method) (pyrosetta.rosetta.utility.options.AnyVectorOptionKey method) (pyrosetta.rosetta.utility.options.BooleanOptionKey method) (pyrosetta.rosetta.utility.options.BooleanVectorOptionKey method) (pyrosetta.rosetta.utility.options.FileOptionKey method) (pyrosetta.rosetta.utility.options.FileVectorOptionKey method) (pyrosetta.rosetta.utility.options.IntegerOptionKey method) (pyrosetta.rosetta.utility.options.IntegerVectorOptionKey method) (pyrosetta.rosetta.utility.options.OptionKey method) (pyrosetta.rosetta.utility.options.PathOptionKey method) (pyrosetta.rosetta.utility.options.PathVectorOptionKey method) (pyrosetta.rosetta.utility.options.RealOptionKey method) (pyrosetta.rosetta.utility.options.RealVectorOptionKey method) (pyrosetta.rosetta.utility.options.ResidueChainVectorOptionKey method) (pyrosetta.rosetta.utility.options.ScalarOptionKey method) (pyrosetta.rosetta.utility.options.StringOptionKey method) (pyrosetta.rosetta.utility.options.StringVectorOptionKey method) (pyrosetta.rosetta.utility.options.VectorOptionKey method) Vector1() (in module pyrosetta) vector1_indices() (in module pyrosetta.util) vector_angle_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) vector_angle_cutoff() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) vector_dist_cut() (pyrosetta.rosetta.core.select.residue_selector.InterGroupInterfaceByVectorSelector method) vector_dist_cutoff() (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictToInterfaceVectorOperation method) vector_normal_to_ring_plane_of_best_fit() (in module pyrosetta.rosetta.numeric.geometry) vector_to_rank() (in module pyrosetta.rosetta.protocols.ligand_docking) VectorOption (class in pyrosetta.rosetta.utility.options) VectorOptionKey (class in pyrosetta.rosetta.utility.options) VectorPoseMover (class in pyrosetta.rosetta.protocols.moves) vectorsEqual() (in module pyrosetta.rosetta.numeric.kinematic_closure) ver() (pyrosetta.rosetta.utility.file.FileName method) verbose() (pyrosetta.rosetta.protocols.matdes.GetRBDOFValues method) (pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter method) (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) (pyrosetta.rosetta.protocols.toolbox.task_operations.RestrictConservedLowDdgOperation method) verbose_sampler() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) verify_against() (pyrosetta.rosetta.protocols.loops.Loops method) version() (pyrosetta.rosetta.core.pack.interaction_graph.HPatchEnergy method) (pyrosetta.rosetta.core.pack.interaction_graph.SurfaceEnergy method) (pyrosetta.rosetta.core.scoring.aa_composition_energy.AACompositionEnergy method) (pyrosetta.rosetta.core.scoring.aa_repeat_energy.AARepeatEnergy method) (pyrosetta.rosetta.core.scoring.hbonds.NPDHBondEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPEnvSmoothEnergy method) (pyrosetta.rosetta.core.scoring.membrane.FaMPSolvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPCbetaEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPEnvEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPLipoEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPNonHelixPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPPairEnergy method) (pyrosetta.rosetta.core.scoring.membrane.MPTMProjPenalty method) (pyrosetta.rosetta.core.scoring.membrane.MPTerminiPenalty method) (pyrosetta.rosetta.core.scoring.methods.BranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.CartesianBondedEnergy method) (pyrosetta.rosetta.core.scoring.methods.ChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.DNA_EnvPairEnergy method) (pyrosetta.rosetta.core.scoring.methods.DirectReadoutEnergy method) (pyrosetta.rosetta.core.scoring.methods.DistanceChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.EnergyMethod method) (pyrosetta.rosetta.core.scoring.methods.GoapEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearBranchEnergy method) (pyrosetta.rosetta.core.scoring.methods.LinearChainbreakEnergy method) (pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy method) (pyrosetta.rosetta.core.scoring.methods.carbohydrates.SugarBackboneEnergy method) (pyrosetta.rosetta.core.scoring.rna.RNA_LowResolutionPotential method) (pyrosetta.rosetta.core.scoring.rna.chemical_shift.RNA_ChemicalShiftEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.AACompositionEnergy method) (pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy method) (pyrosetta.rosetta.protocols.rna.AlignmentEnergy method) (pyrosetta.rosetta.utility.file.FileName method) vertex() (pyrosetta.rosetta.core.chemical.ICoorAtomID method) (pyrosetta.rosetta.core.chemical.ResidueConnection method) vertex_already_reached() (pyrosetta.rosetta.core.pack.interaction_graph.DoubleLazyInteractionGraph method) vertex_count() (pyrosetta.rosetta.core.scoring.power_diagram.PowerDiagram method) vertex_exists() (in module pyrosetta.rosetta.protocols.forge.methods) vertex_xyz_from_generators() (in module pyrosetta.rosetta.core.scoring.power_diagram) vertices() (pyrosetta.rosetta.core.scoring.PDatom method) (pyrosetta.rosetta.core.scoring.power_diagram.PDsphere method) VicinityPerturber (class in pyrosetta.rosetta.protocols.kinematic_closure.perturbers) VicinitySamplingKinematicPerturber (class in pyrosetta.rosetta.protocols.loops.loop_closure.kinematic_closure) view_constraints_in_pymol() (pyrosetta.rosetta.protocols.metal_interface.AddZincSiteConstraints method) virtual_sidechain() (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) virtual_sugar_do_minimize() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtual_sugar_do_screens() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtual_sugar_keep_base_fixed() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtual_sugar_legacy_mode() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtual_to_real() (pyrosetta.rosetta.core.pose.Pose method) virtual_type_for_conf() (in module pyrosetta.rosetta.core.conformation) virtual_type_for_pose() (in module pyrosetta.rosetta.core.pose) virtualize_5prime_phosphates() (in module pyrosetta.rosetta.core.pose.rna) virtualize_bulges() (in module pyrosetta.rosetta.protocols.rna.denovo) virtualize_free_rna_moieties() (in module pyrosetta.rosetta.protocols.stepwise.modeler.rna) virtualize_packable_moieties_in_screening_pose() (pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions method) virtualize_side_chains() (in module pyrosetta.rosetta.protocols.stepwise.modeler) VirtualizeAll (class in pyrosetta.rosetta.core.chemical) visible() (pyrosetta.rosetta.basic.Tracer method) visit() (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTNode method) (pyrosetta.rosetta.numeric.expression_parser.ASTPrinter method) (pyrosetta.rosetta.numeric.expression_parser.ASTVisitor method) (pyrosetta.rosetta.numeric.expression_parser.ArithmeticASTValue method) (pyrosetta.rosetta.numeric.expression_parser.ExpressionCreator method) visualize_fold_tree() (in module pyrosetta.rosetta.core.kinematics) VisualizeEmbeddingMover (class in pyrosetta.rosetta.protocols.membrane.visualize) VisualizeEmbeddingMoverCreator (class in pyrosetta.rosetta.protocols.membrane.visualize) VisualizeMembraneMover (class in pyrosetta.rosetta.protocols.membrane.visualize) VisualizeMembraneMoverCreator (class in pyrosetta.rosetta.protocols.membrane.visualize) vl_vh_orientation_coords() (in module pyrosetta.rosetta.protocols.antibody) VLB (class in pyrosetta.rosetta.protocols.protein_interface_design.movers) vlb() (pyrosetta.rosetta.protocols.fldsgn.SheetRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.constraints.InverseRotamersRCG method) (pyrosetta.rosetta.protocols.forge.constraints.InvrotTreeRCG method) (pyrosetta.rosetta.protocols.forge.remodel.GenericRemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.RemodelConstraintGenerator method) (pyrosetta.rosetta.protocols.forge.remodel.ResidueVicinityRCG method) VMaxBy (class in pyrosetta.rosetta.protocols.pack_daemon) VMinBy (class in pyrosetta.rosetta.protocols.pack_daemon) vol() (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) volume() (pyrosetta.rosetta.core.scoring.FACTSRsdTypeInfo method) (pyrosetta.rosetta.utility.file.FileName method) (pyrosetta.rosetta.utility.file.PathName method) VoxelSetIterator (class in pyrosetta.rosetta.protocols.match) VoxelSpacingMultifunc (class in pyrosetta.rosetta.protocols.electron_density) VoxelSpacingRefinementMover (class in pyrosetta.rosetta.protocols.electron_density) vrt1() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method) vrt2() (pyrosetta.rosetta.core.scoring.power_diagram.PDinter method)