- v -

• V2Parser() : core::chemical::sdf::V2Parser
• V3Parser() : core::chemical::sdf::V3Parser
• v_begin() : protocols::loops::Loops
• v_end() : protocols::loops::Loops
• valid() : core::id::AtomID , core::scoring::DimerPairing , core::id::StubID , protocols::id::AlignmentID , protocols::fldsgn::topology::DimerPairing , core::graph::ArrayPoolElement< T > , core::id::DOF_ID , protocols::fldsgn::topology::DimerPairing , protocols::jd2::archive::Batch , core::id::JumpID , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover , core::graph::EdgeListIterator , core::id::NamedAtomID , protocols::simple_moves::ExtendedPoseMover , core::id::NamedStubID , core::graph::EdgeListConstIterator , core::id::TorsionID , core::kinematics::Edge
• 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_frag_set() : protocols::features::helixAssembly::HelixBundleFeatures
• valid_peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_receptor_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_ref_start_struct() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_ss() : protocols::simple_moves::ClassicFragmentMover
• validate_downstream_orientation_atoms() : protocols::match::MatcherTask
• validate_input() : core::sequence::Aligner
• validate_ramachandran_hash() : protocols::features::BetaTurnDetectionFeatures
• vall_memory_usage() : protocols::forge::components::VarLengthBuild
• 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::io::silent::SilentEnergy , core::scoring::hbonds::FadeInterval
• value_deriv() : core::scoring::hbonds::FadeInterval
• value_passes() : protocols::enzdes::ValueEvaluator
• value_set() : protocols::pack_daemon::InSetExpression
• 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
• variable_expression() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• VariableVectorExpression() : protocols::pack_daemon::VariableVectorExpression
• VarianceStatisticsArchive() : protocols::jd2::archive::VarianceStatisticsArchive
• variant_types() : core::chemical::ResidueType , core::pose::MiniPose
• variant_types_list() : core::pose::MiniPose
• variants_match() : core::chemical::ResidueType
• VarLengthBuild() : protocols::forge::components::VarLengthBuild
• VARS_str_parser() : protocols::sparta::GDB
• vary_bond_geometry() : protocols::rna::RNA_Minimizer , protocols::simple_moves::ConstrainToIdealMover
• vbpos() : protocols::motifs::MotifHit
• vdw_atom_list() : core::scoring::rna::RNA_AtomVDW
• vdw_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• VDW_Energy() : core::scoring::methods::VDW_Energy
• VDW_rep_screen() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• VDW_rep_screen_with_act_pose() : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• VDW_RepScreeninfo() : protocols::swa::rna::VDW_RepScreeninfo
• VdwGrid() : protocols::qsar::scoring_grid::VdwGrid
• 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
• vector_angle_cutoff() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• vector_dist_cutoff() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• vector_values() : protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::IterativeVectorExpression
• 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
• verbose() : protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter
• verify_against() : protocols::loops::Loops
• verify_chain_setup() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• verify_parameters_() : core::scoring::constraints::MixtureFunc
• verify_patch_areas_correct() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• verify_phipsi_bins() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• verify_probabilities_or_die() : protocols::nonlocal::BiasedFragmentMover
• verify_protonated_H1_adenosine_variants() : protocols::swa::rna::StepWiseRNA_PoseSetup
• verify_remote_daemon_set_initialization_successful() : protocols::pack_daemon::DynamicAggregateFunction
• verify_variable_name_or_throw() : protocols::pack_daemon::DynamicAggregateFunction
• verify_vector_arguments() : protocols::pack_daemon::DynamicAggregateFunction
• version() : core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::hackaro::HackAroEnergy , core::scoring::etable::AnalyticEtableEnergy , core::scoring::methods::CenPairEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::dna::DNATorsionEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::methods::RMS_Energy , core::scoring::constraints::ConstraintsEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::saxs::FastSAXSEnergy , core::pack::dunbrack::DunbrackEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::methods::VDW_Energy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::BurialEnergy , protocols::scoring::methods::saxs::PDDFEnergy , core::scoring::sym_e::symEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , protocols::scoring::methods::EnsembleEnergy , core::scoring::methods::WaterAdductHBondEnergy , protocols::scoring::methods::pcs::PCS_Energy , core::scoring::nv::NVscore , core::scoring::interface::DDPscore , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::methods::SA_Energy , core::scoring::methods::SuckerEnergy , protocols::scoring::methods::InterchainEnvEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::pack::interaction_graph::HPatchEnergy , protocols::scoring::methods::pcs2::PcsEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::rna::RNA_DataBackboneEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::rna::RNA_Mg_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::MembraneLipo , protocols::scoring::methods::InterchainPairEnergy , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::methods::LK_BallEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::saxs::SAXSEnergyCreatorFA , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::CustomAtomPairEnergy , protocols::features::ProteinSilentReport , core::scoring::methods::CenHBEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::hbonds::HBondEnergy , protocols::fldsgn::potentials::AACompositionEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::saxs::SAXSEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , protocols::features::Report , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::hackelec::HackElecEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::pHEnergy , core::scoring::saxs::SAXSEnergyCreatorCEN , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::packing::HolesEnergy , core::scoring::packing::SurfEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::ReferenceEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , protocols::scoring::methods::SpecialRotamerEnergy , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::EnvEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::LK_hack , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::rna::RNA_BulgeEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::EnergyMethod , core::scoring::methods::DipolarCouplingEnergy
• vertex_already_reached() : core::pack::interaction_graph::InteractionGraphBase
• very_far_away() : protocols::simple_moves::symmetry::SymmetrySlider
• VicinitySamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• view() : protocols::flexpep_docking::FlexPepDockingProtocol
• viols() : core::scoring::constraints::SkipViolFunc , core::scoring::constraints::CountViolFunc
• VIP_Mover() : protocols::vip::VIP_Mover
• VIP_Report() : protocols::vip::VIP_Report
• VirtualCoordinate() : core::conformation::symmetry::VirtualCoordinate
• VirtualCoordinates() : core::conformation::symmetry::VirtualCoordinates
• visit() : protocols::simple_moves::TailsScoreMover , protocols::sic_dock::CorrectionVisitor , core::conformation::AddEdgeVisitor< Vertex, Edge > , protocols::sic_dock::CBScoreVisitor
• 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
• volume() : protocols::noesy_assign::CrossPeak , core::scoring::FACTSResidueInfo
• VoxelSetIterator() : protocols::match::VoxelSetIterator