- v -

• v_angle_width() : core::scoring::magnesium::MgKnowledgeBasedPotential
• v_begin() : protocols::loops::Loops
• v_end() : protocols::loops::Loops
• valence_electrons_p() : core::chemical::ElectronConfiguration
• valence_electrons_s() : core::chemical::ElectronConfiguration
• valence_electrons_sp() : core::chemical::ElectronConfiguration
• valence_electrons_spd() : core::chemical::ElectronConfiguration
• valid() : core::id::AtomID , core::id::DOF_ID , core::id::JumpID , core::id::NamedAtomID , core::id::NamedStubID , core::id::StubID , core::id::TorsionID , core::kinematics::Edge , core::scoring::DimerPairing , core::scoring::motif::ResPairMotif , protocols::fldsgn::topology::DimerPairing , protocols::jd2::archive::Batch , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover , protocols::pose_creation::ExtendedPoseMover
• valid_anchors() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_basestep_start() : protocols::dna::DNAParameters
• valid_chain_info() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_ends() : core::scoring::dssp::StrandPairing
• valid_index() : core::grid::CartGrid< T >
• valid_names() : protocols::constraint_generator::ConstraintsMap
• valid_names_string() : protocols::constraint_generator::ConstraintsMap
• valid_next_grid_point() : core::scoring::nmr::NMRGridSearch
• valid_peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_receptor_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_ref_start_struct() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_res_pair() : core::scoring::methods::ArgCationPiEnergy
• valid_ss() : protocols::simple_moves::ClassicFragmentMover
• valid_surface_pose() : protocols::surface_docking::SurfaceDockingProtocol
• validate() : protocols::environment::claims::JumpClaim
• validate_beta() : core::scoring::ScoreFunctionFactory
• validate_bundle() : protocols::features::helixAssembly::HelixBundleFeatures
• validate_downstream_orientation_atoms() : protocols::match::MatcherTask
• validate_dunbrack_binary() : core::pack::dunbrack::RotamerLibrary
• validate_input() : core::sequence::Aligner
• validate_input_script_against_xsd() : protocols::rosetta_scripts::RosettaScriptsParser
• validate_ramachandran_hash() : protocols::features::BetaTurnDetection
• validate_residue_type() : core::chemical::MutableResidueType
• validate_talaris() : core::scoring::ScoreFunctionFactory
• validate_template() : protocols::hybridization::HybridizeProtocol
• vall_key() : protocols::frag_picker::VallChunk
• vall_memory_usage() : protocols::forge::components::VarLengthBuild
• vall_torsions_file() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• VallChunk() : protocols::frag_picker::VallChunk
• vallChunksFromLibraries() : protocols::frag_picker::VallProvider
• vallChunksFromLibrary() : protocols::frag_picker::VallProvider
• VallData() : protocols::frags::VallData
• VallFragmentEval() : core::fragment::picking_old::vall::eval::VallFragmentEval
• VallFragmentGen() : core::fragment::picking_old::vall::gen::VallFragmentGen
• VallFragmentScore() : core::fragment::picking_old::vall::scores::VallFragmentScore
• VallLibrarian() : core::fragment::picking_old::vall::VallLibrarian
• vallNumLines() : protocols::frag_picker::VallProvider
• VallProvider() : protocols::frag_picker::VallProvider
• VallResidue() : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• value() : core::conformation::parametric::BooleanValuedParameter , core::conformation::parametric::RealValuedParameter , core::conformation::parametric::RealVectorValuedParameter , core::conformation::parametric::SizeValuedParameter , core::conformation::parametric::SizeVectorValuedParameter , core::io::silent::SilentEnergy , core::pose::rna::RNA_Reactivity , core::scoring::hbonds::FadeInterval , protocols::stepwise::sampler::StepWiseSamplerOneValue
• value_deriv() : core::scoring::hbonds::FadeInterval
• value_is_in_map() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser
• value_max() : core::conformation::parametric::RealValuedParameter
• value_min() : core::conformation::parametric::RealValuedParameter
• value_passes() : protocols::enzdes::ValueEvaluator
• value_range() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• value_samples() : core::conformation::parametric::RealValuedParameter
• value_set() : protocols::pack_daemon::InSetExpression
• value_was_set() : core::conformation::parametric::Parameter
• ValueEvaluator() : protocols::enzdes::ValueEvaluator
• values_for_aa() : core::sequence::MatrixScoringScheme
• values_from_pose() : protocols::comparative_modeling::features::ResidueFeature , protocols::comparative_modeling::features::SSFeature , protocols::comparative_modeling::features::TorsionFeature
• VanillaJobDistributor() : protocols::jd3::job_distributors::VanillaJobDistributor
• variable_expression() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• VariableVectorExpression() : protocols::pack_daemon::VariableVectorExpression
• VarianceStatisticsArchive() : protocols::jd2::archive::VarianceStatisticsArchive
• variant_exceptions() : core::chemical::ResidueTypeFinder
• variant_type_enums() : core::chemical::ResidueTypeBase
• variant_types() : core::chemical::ResidueTypeBase , core::pose::MiniPose
• variant_types_list() : core::pose::MiniPose
• variants() : core::chemical::ResidueTypeFinder
• variants_in_sets() : core::chemical::ResidueTypeFinder
• VarLengthBuild() : protocols::forge::components::VarLengthBuild
• VARS_str_parser() : protocols::sparta::GDB
• vars_to_dofs() : protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• vars_to_params() : protocols::helical_bundle::FitSimpleHelixMultiFunc
• VarSolDistSasaCalculator() : protocols::vardist_solaccess::VarSolDistSasaCalculator
• VarSolDRotamerDots() : protocols::vardist_solaccess::VarSolDRotamerDots
• vary_bond_geometry() : core::import_pose::options::RNA_MinimizerOptions , protocols::rna::movers::ErraserMinimizerMover , protocols::simple_moves::ConstrainToIdealMover
• vary_loop_length_frequency() : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• vary_polar_hydrogen_geometry() : protocols::stepwise::options::StepWiseBasicOptions
• vary_rna_bond_geometry() : protocols::stepwise::options::StepWiseBasicOptions
• vary_stepsize() : protocols::docking::SlideIntoContact , protocols::rigid::RigidBodyTransMover
• VaryLoopLengthMover() : protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover
• vbpos() : protocols::motifs::MotifHit
• VDDistanceMatrix() : core::chemical::VDDistanceMatrix
• vdw_atom_list() : core::scoring::rna::RNA_AtomVDW
• VDW_BinScreener() : protocols::stepwise::screener::VDW_BinScreener
• VDW_CachedRepScreenInfo() : protocols::scoring::VDW_CachedRepScreenInfo
• vdw_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• VDW_Energy() : core::scoring::vdwaals::VDW_Energy
• VDW_Grid() : core::pose::rna::VDW_Grid
• VDW_GridEnergy() : protocols::scoring::VDW_GridEnergy
• VDW_rep_alignment_RMSD_CUTOFF() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• VDW_rep_delete_matching_res() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• VDW_rep_screen() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• vdw_rep_screen_include_sidechains() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• VDW_rep_screen_info() : core::import_pose::options::RNA_FragmentMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions
• VDW_rep_screen_info_list() : protocols::scoring::VDW_CachedRepScreenInfo
• VDW_rep_screen_physical_pose_clash_dist_cutoff() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• VDW_rep_screen_with_act_pose() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• VDW_RepScreenInfo() : core::pose::rna::VDW_RepScreenInfo
• VDW_screen_bin() : protocols::scoring::VDW_CachedRepScreenInfo
• vdw_type() : core::scoring::VdWTinkerResidueInfo
• vdw_weight() : core::scoring::vdwaals::VDWTrieEvaluator
• VDWAtom() : core::scoring::vdwaals::VDWAtom
• VdwGrid() : protocols::qsar::scoring_grid::VdwGrid
• VdWTinkerEnergy() : core::scoring::methods::VdWTinkerEnergy
• VdWTinkerPoseInfo() : core::scoring::VdWTinkerPoseInfo
• VdWTinkerPotential() : core::scoring::VdWTinkerPotential
• VdWTinkerResidueInfo() : core::scoring::VdWTinkerResidueInfo
• VdWTinkerResPairMinData() : core::scoring::methods::VdWTinkerResPairMinData
• VdWTinkerRotamerSetInfo() : core::scoring::VdWTinkerRotamerSetInfo
• VDWTrieCountPair1B() : core::scoring::vdwaals::VDWTrieCountPair1B
• VDWTrieEvaluator() : core::scoring::vdwaals::VDWTrieEvaluator
• Vec3Abs() : protocols::sparta::PDB
• Vec3Add() : protocols::sparta::PDB
• Vec3Copy() : protocols::sparta::PDB
• Vec3Cross() : protocols::sparta::PDB
• Vec3DiffAbs() : protocols::sparta::PDB
• Vec3Norm() : protocols::sparta::PDB
• Vec3Scalar() : protocols::sparta::PDB
• Vec3Scale() : protocols::sparta::PDB
• Vec3ScaleAdd() : protocols::sparta::PDB
• Vec3Sub() : protocols::sparta::PDB
• Vec3Zero() : protocols::sparta::PDB
• vec_ex() : protocols::pack_daemon::VectorFunction
• vec_ex1() : protocols::pack_daemon::VectorFunction2
• vec_ex2() : protocols::pack_daemon::VectorFunction2
• vecAB() : protocols::surface_docking::SurfaceParameters
• vecAC() : protocols::surface_docking::SurfaceParameters
• vector_angle_cut() : core::select::residue_selector::InterGroupInterfaceByVectorSelector , protocols::simple_filters::DomainInterfaceFilter
• vector_angle_cutoff() : protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictToInterfaceVectorOperation
• vector_dist_cut() : core::select::residue_selector::InterGroupInterfaceByVectorSelector , protocols::simple_filters::DomainInterfaceFilter
• vector_dist_cutoff() : protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictToInterfaceVectorOperation
• vector_intersect() : core::scoring::BondOrderParser
• vector_sum() : protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• vector_union() : core::scoring::BondOrderParser
• vector_values() : protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VectorExpression
• VectorExpression() : protocols::pack_daemon::VectorExpression
• VectorExpressionCreator() : protocols::pack_daemon::VectorExpressionCreator
• VectorFunction() : protocols::pack_daemon::VectorFunction
• VectorFunction2() : protocols::pack_daemon::VectorFunction2
• VectorPair() : protocols::hotspot_hashing::VectorPair
• VectorPoseFilter() : protocols::filters::VectorPoseFilter
• VectorPoseJobDistributor() : protocols::jd2::VectorPoseJobDistributor
• VectorPoseMover() : protocols::moves::VectorPoseMover
• vel() : protocols::md::MDBase
• VelocityVerlet_Integrator() : protocols::md::CartesianMD
• verbose() : core::import_pose::options::RNA_BasicOptions , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::hbnet::HBNet , protocols::magnesium::MgHydrater , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::ContactMolecularSurfaceFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::StepWiseSampleAndScreen , protocols::task_operations::RestrictConservedLowDdgOperation , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::StoreCompoundTaskMover
• verbose_sampler() : protocols::stepwise::options::StepWiseBasicOptions
• verbose_scores() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• verify() : protocols::environment::ProtectedConformation
• verify_against() : protocols::loops::Loops
• verify_backbone() : protocols::environment::ProtectedConformation
• verify_bb_bins() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• verify_chain_setup() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• verify_jump() : protocols::environment::ProtectedConformation
• verify_parameters_() : core::scoring::func::MixtureFunc
• verify_patch_areas_correct() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• verify_phipsi_bins() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• verify_probabilities_or_die() : protocols::nonlocal::BiasedFragmentMover
• verify_protonated_H1_adenosine_variants() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• verify_remote_daemon_set_initialization_successful() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• verify_variable_name_or_throw() : protocols::pack_daemon::DynamicAggregateFunction
• verify_vector_arguments() : protocols::pack_daemon::DynamicAggregateFunction
• version() : core::energy_methods::DEEREnergy , core::io::rna::RDAT , core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty , core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::aa_repeat_energy::AARepeatEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::cryst::XtalMLEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::hbonds::NPDHBondEnergy , core::scoring::interface_::DDPscore , core::scoring::lkball::LK_BallEnergy , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::magnesium::MgEnergy , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPHelicalityEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPResidueLipophilicityEnergy , core::scoring::membrane::MPSpanAngleEnergy , core::scoring::membrane::MPSpanInsertionEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty , core::scoring::methods::Abego , core::scoring::methods::ArgCationPiEnergy , core::scoring::methods::AromaticBackboneRestraintEnergy , core::scoring::methods::AspartimidePenaltyEnergy , core::scoring::methods::BranchEnergy , core::scoring::methods::Burial_v2Energy , core::scoring::methods::BurialEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::CovalentLabelingEnergy , core::scoring::methods::CovalentLabelingFAEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::D2H_SA_Energy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::DNA_EnvPairEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::FreeDOF_Energy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GenericBondedEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HRF_MSLabelingEnergy , core::scoring::methods::HRFDynamicsEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::HydroxylTorsionEnergy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearBranchEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MissingEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MotifDockEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OtherPoseEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::P_AA_ss_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PointWaterEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RingClosureEnergy , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SASAEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SplitUnfoldedTwoBodyEnergy , core::scoring::methods::SSElementMotifContactEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::WaterSpecificEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::mhc_epitope_energy::MHCEpitopeEnergy , core::scoring::netcharge_energy::NetChargeEnergy , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_LowResolutionPotential , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_PartitionEnergy , core::scoring::rna::RNA_StubCoordinateEnergy , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::RNP_LowResEnergy , core::scoring::rna::RNP_LowResPairDistEnergy , core::scoring::rna::RNP_LowResStackEnergy , core::scoring::rna::StackElecEnergy , core::scoring::rna::TNA_SuiteEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , core::scoring::saxs::SAXSEnergyCreatorCEN , core::scoring::saxs::SAXSEnergyCreatorFA , core::scoring::sym_e::symEnergy , core::scoring::util_methods::DumpTrajectoryEnergy , core::scoring::vdwaals::VDW_Energy , protocols::features::ProteinSilentReport , protocols::features::Report , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::membrane::scoring::FaWaterToBilayerEnergy , protocols::nmr::pcs::PCSEnergy , protocols::nmr::pre::PREEnergy , protocols::nmr::rdc::RDCEnergy , protocols::rna::AlignmentEnergy , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::saxs::PDDFEnergy , protocols::scoring::methods::SpecialRotamerEnergy , protocols::scoring::methods::TargetClashEnergy , protocols::scoring::VDW_GridEnergy , protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::hashing::EdgeMapGenerator
• vertex() : core::chemical::MutableResidueConnection
• vertex_already_reached() : core::pack::interaction_graph::InteractionGraphBase
• vertex_count() : core::scoring::power_diagram::PowerDiagram , core::scoring::SASAPotential
• vertices() : core::scoring::PDatom , core::scoring::power_diagram::PDsphere
• very_far_away() : protocols::symmetry::SymmetrySlider
• VicinityPerturber() : protocols::kinematic_closure::perturbers::VicinityPerturber
• VicinitySamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• view() : protocols::flexpep_docking::FlexPepDockingProtocol
• view_constraints_in_pymol() : protocols::metal_interface::AddZincSiteConstraints
• violates() : protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirement , protocols::legacy_sewing::sampling::requirements::LegacyGlobalRequirement , protocols::legacy_sewing::sampling::requirements::LegacyIntraSegmentRequirement , protocols::legacy_sewing::sampling::requirements::LegacyRequirementSet , protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentDsspRequirement , protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirement
• viols() : core::scoring::func::CountViolFunc , core::scoring::func::SkipViolFunc
• VIP_Mover() : protocols::vip::VIP_Mover
• VIP_Report() : protocols::vip::VIP_Report
• VirtResClaim() : protocols::environment::claims::VirtResClaim
• virtual_anchor_attachment_points() : core::import_pose::RNA_DeNovoParameters
• virtual_anomeric_carbon_index() : core::chemical::carbohydrates::CarbohydrateInfo
• virtual_cyclic_oxygen_index() : core::chemical::carbohydrates::CarbohydrateInfo
• virtual_sidechain() : core::pack::rotamers::SingleResidueRotamerLibrary
• virtual_sugar_do_minimize() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• virtual_sugar_do_screens() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• virtual_sugar_keep_base_fixed() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• virtual_sugar_legacy_mode() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• virtual_to_real() : core::pose::Pose
• VirtualCoordinate() : core::conformation::symmetry::VirtualCoordinate
• virtualize_distal_partition() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• virtualize_packable_moieties_in_screening_pose() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• virtualize_poor_scoring_o2prime_hydrogens() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• virtualize_sugar_and_backbone_at_moving_res() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• VirtualizeAll() : core::chemical::VirtualizeAll
• VirtualizeSidechain() : core::chemical::VirtualizeSidechain
• VirtualRootMover() : protocols::simple_moves::VirtualRootMover
• VirtualSugarJustInTimeInstantiator() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• VirtualSugarSampler() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• VirtualSugarSamplerFromStringList() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList
• visit() : core::conformation::AddEdgeVisitor< Vertex, Edge > , core::environment::FoldTreeSketch , core::select::residue_selector::SelectorLogicParser , protocols::sic_dock::CBScoreVisitor , protocols::sic_dock::CorrectionVisitor , protocols::simple_moves::TailsScoreMover
• visited() : core::environment::FoldTreeSketch::Node
• visualize_at_depth() : core::scoring::atomic_depth::AtomicDepth
• visualize_voxel_grid() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• VisualizeEmbeddingMover() : protocols::membrane::visualize::VisualizeEmbeddingMover
• VisualizeMembraneMover() : protocols::membrane::visualize::VisualizeMembraneMover
• vl_vh_cut() : protocols::splice::SpliceOutAntibody
• vlb() : protocols::forge::remodel::RemodelConstraintGenerator
• VLB() : protocols::protein_interface_design::movers::VLB
• VMax() : protocols::pack_daemon::VMax
• VMaxBy() : protocols::pack_daemon::VMaxBy
• VMin() : protocols::pack_daemon::VMin
• VMinBy() : protocols::pack_daemon::VMinBy
• voids_penalty_energy_cone_distance_cutoff() : core::scoring::methods::EnergyMethodOptions
• voids_penalty_energy_cone_dotproduct_cutoff() : core::scoring::methods::EnergyMethodOptions
• voids_penalty_energy_containing_cones_cutoff() : core::scoring::methods::EnergyMethodOptions
• voids_penalty_energy_disabled_except_during_packing() : core::scoring::methods::EnergyMethodOptions
• voids_penalty_energy_voxel_grid_padding() : core::scoring::methods::EnergyMethodOptions
• voids_penalty_energy_voxel_size() : core::scoring::methods::EnergyMethodOptions
• VoidsPenaltyEnergy() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy
• VoidsPenaltyVoxelGrid() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• volume() : core::scoring::FACTSRsdTypeInfo , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::noesy_assign::CrossPeak
• voxel_volume() : core::scoring::electron_density::ElectronDensity
• VoxelGridPoint() : core::scoring::nmr::VoxelGridPoint
• VoxelGridPoint_AA() : core::scoring::nmr::VoxelGridPoint_AA
• VoxelSetIterator() : protocols::match::VoxelSetIterator
• VoxelSpacingMultifunc() : protocols::electron_density::VoxelSpacingMultifunc
• VoxelSpacingRefinementMover() : protocols::electron_density::VoxelSpacingRefinementMover
• vrt1() : core::scoring::PDinter , core::scoring::power_diagram::PDinter
• vrt2() : core::scoring::PDinter , core::scoring::power_diagram::PDinter
• vrt_label() : protocols::environment::claims::VirtResClaim