- v -

• v : core::kinematics::Stub , core::optimization::EItem
• V : core::scoring::electron_density::ElectronDensity
• v_ : core::optimization::Particle
• V_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• v_angle_baseline : core::scoring::magnesium::MgEnergy
• v_angle_width2_ : core::scoring::magnesium::MgEnergy
• v_angle_width_ : core::scoring::magnesium::MgEnergy , core::scoring::magnesium::MgKnowledgeBasedPotential
• v_indexes : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• v_max_ : core::optimization::ParticleSwarmMinimizer
• val : protocols::hybridization::TMalign
• valence_electrons_sp_ : core::chemical::ElectronConfiguration
• valence_electrons_spd_ : core::chemical::ElectronConfiguration
• valence_quantum_number_ : core::chemical::ElectronConfiguration
• valid : core::fragment::picking_old::concepts::Extent< PageIterator > , core::scoring::sc::_RESULTS
• valid_ : core::fragment::FragData , core::scoring::DimerPairing , protocols::fldsgn::topology::DimerPairing
• valid_chain_bounds_ : protocols::flexpep_docking::FlexPepDockingFlags
• valid_dssp_codes_ : protocols::sewing::sampling::requirements::SegmentDsspRequirement
• valid_loop_file_keys_ : protocols::loops::JSONFormattedLoopsFileReader
• valid_peptide_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• valid_receptor_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• valid_ref_start_struct_ : protocols::flexpep_docking::FlexPepDockingFlags
• valid_segments_ : protocols::backrub::BackrubSidechainMover
• valid_variable_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• vall_ : core::fragment::picking_old::FragmentLibraryManager
• vall_edge_is_base_pairing_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_end_line_ : protocols::frag_picker::VallProvider
• vall_is_chainbreak_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_key_ : protocols::frag_picker::VallChunk
• vall_keys_ : protocols::frag_picker::VallProvider
• vall_last_residue_key_ : protocols::frag_picker::VallProvider
• vall_makes_canonical_base_pair_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_memory_usage_ : protocols::forge::components::VarLengthBuild
• vall_name_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_non_main_chain_sugar_coords_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_non_main_chain_sugar_coords_defined_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_secstruct_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_sequence_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_size_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_start_line_ : protocols::frag_picker::VallProvider
• vall_torsions_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vallResidueIndex_ : protocols::frag_picker::FragmentCandidate
• value : core::io::pdb::Field , core::io::RemarkInfo , protocols::stepwise::modeler::rna::Torsion_Info
• value_ : core::io::silent::SilentEnergy , core::scoring::rna::data::RNA_Reactivity , protocols::filters::ContingentFilter , protocols::qsar::qsarPoint , protocols::wum::find_SilentStructOPs
• value_list_cached_ : protocols::stepwise::sampler::StepWiseSamplerOneValueComb
• value_range_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• value_set_ : protocols::pack_daemon::InSetExpression
• value_type_ : core::scoring::methods::SplitUnfoldedTwoBodyEnergy , protocols::simple_moves::AddJobPairData
• values_ : protocols::filters::CalculatorFilter , protocols::filters::IfThenFilter , protocols::stepwise::sampler::StepWiseSamplerOneValue
• vanilla_options_ : protocols::abinitio::IterativeBase , protocols::jd2::BatchJobInputter
• var_type_ : protocols::normalmode::NormalModeMultifunc
• variable_expression_map_ : protocols::pack_daemon::EntityFunc
• variable_expressions_ : protocols::pack_daemon::DynamicAggregateFunction
• variable_expressions_for_npd_properties_ : protocols::pack_daemon::DynamicAggregateFunction
• variable_expressions_for_states_ : protocols::pack_daemon::DynamicAggregateFunction
• variable_name_2_variable_exp_index_ : protocols::pack_daemon::DynamicAggregateFunction
• variable_names_dec_line_ : protocols::pack_daemon::DynamicAggregateFunction
• variance_archive_ : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• variant_ : core::chemical::DeleteVariantType
• variant_exceptions_ : core::chemical::ResidueTypeFinder
• variant_type_status_ : core::chemical::ResidueProperties
• variant_types_list_ : core::pose::MiniPose
• variants_ : core::chemical::Selector_MATCH_VARIANTS , core::chemical::Selector_VARIANT_TYPE
• variants_in_sets_ : core::chemical::ResidueTypeFinder
• various_length_poses_ : protocols::simple_moves::GunnCost
• VARS : protocols::sparta::GDB
• vars_ : protocols::pack_daemon::VariableVectorExpression
• vars_index_to_torsion_id_ : protocols::ncbb::SecStructMinimizeMultiFunc
• VARS_str : protocols::sparta::GDB
• VarsNumber : protocols::sparta::GDB
• vary_bond_angles_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• vary_bond_geometry_ : protocols::farna::options::RNA_MinimizerOptions
• vary_bond_geometry_frequency_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• vary_ca_bond_angles_ : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• vary_cutpoints_ : protocols::anchored_design::AnchoredDesignMover
• vary_loop_length_frequency_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• vary_loop_length_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• vary_polar_hydrogen_geometry_ : protocols::stepwise::options::StepWiseBasicOptions
• vary_rna_bond_geometry_ : protocols::stepwise::options::StepWiseBasicOptions
• vary_stepsize_ : protocols::docking::SlideIntoContact , protocols::rigid::RigidBodyTransMover
• vbpos_ : protocols::motifs::MotifHit
• vd_ : core::chemical::ICoorAtomID
• vd_to_index_ : core::chemical::ResidueType
• vdw_ : core::scoring::vdwaals::VDWTrieEvaluator
• VDW_align_res : protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• VDW_bin_checker_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::StepWiseConnectionSampler
• vdw_bin_checker_ : protocols::stepwise::screener::VDW_BinScreener
• vdw_calculation_annotated_sequence_ : core::scoring::rna::RNA_ScoringInfo
• vdw_delta_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• vdw_depth_ : core::scoring::VdWTinkerPotential
• VDW_ignore_res : protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• vdw_params : protocols::relax::CentroidRelax::parameters
• VDW_pose : protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• VDW_RAD : protocols::sparta::PDB
• vdw_radius_ : core::scoring::VdWTinkerPotential
• vdw_reduce_ : core::scoring::VdWTinkerPotential
• VDW_rep_alignment_RMSD_CUTOFF_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• VDW_rep_delete_matching_res_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• VDW_rep_ignore_matching_res_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• VDW_rep_screen_info_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::options::StepWiseBasicOptions
• VDW_rep_screen_info_list_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker , protocols::stepwise::modeler::rna::checker::VDW_CachedRepScreenInfo
• VDW_rep_screen_physical_pose_clash_dist_cutoff_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• VDW_rep_screen_with_physical_pose_verbose_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• vdw_scale_factor_ : core::scoring::rna::RNA_VDW_Energy , core::scoring::vdwaals::VDW_Energy , protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• vdw_score_type_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• VDW_screen_bin_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker , protocols::stepwise::modeler::rna::checker::VDW_CachedRepScreenInfo
• vdw_suffix_ : core::scoring::AtomVDW
• vdw_tinker_potential_ : core::scoring::ScoringManager
• vdw_type_ : core::scoring::VdWTinkerResidueInfo
• vdw_weight_ : core::scoring::vdwaals::VDWTrieEvaluator
• VDW_weight_ : protocols::anchored_design::AnchorMoversData
• vdwcut_ : protocols::simple_moves::CombinePoseMover
• vdWpen : protocols::pockets::PocketExemplarMultifunc
• vec_ex1_ : protocols::pack_daemon::VectorFunction2
• vec_ex2_ : protocols::pack_daemon::VectorFunction2
• vec_ex_ : protocols::pack_daemon::VectorFunction
• vec_exclude_residues_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• vec_exclude_residues_changed_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• vec_exclude_residues_exists_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• vec_filename_ : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• vec_filename_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• vec_individual_weight_ : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• vec_individual_weight_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• vecAB_ : protocols::surface_docking::SurfaceParameters
• vecAC_ : protocols::surface_docking::SurfaceParameters
• vector1_loopsop_having_cdr_ : protocols::antibody::AntibodyInfo
• vector_angle_cut_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector , protocols::simple_filters::DomainInterfaceFilter
• vector_angle_cutoff_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• vector_dist_cut_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector , protocols::simple_filters::DomainInterfaceFilter
• vector_dist_cutoff_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• vector_expression_map_ : protocols::pack_daemon::DynamicAggregateFunction
• vector_variable_names_dec_line_ : protocols::pack_daemon::DynamicAggregateFunction
• vecx : protocols::loophash::LegacyLeapIndex
• vecy : protocols::loophash::LegacyLeapIndex
• vecz : protocols::loophash::LegacyLeapIndex
• vel_ : protocols::md::MDBase
• velocity : protocols::cartesian::CartesianAtom
• verbose_ : core::io::silent::SilentFileData , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_TorsionPotential , core::scoring::rna::StackElecEnergy , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::cryst::ReportGradientsMover , protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc , protocols::farna::movers::RNA_LoopCloser , protocols::farna::MultipleDomainMover , protocols::farna::options::RNA_BasicOptions , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::magnesium::MgHydrater , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::rbsegment_relax::SequenceShiftMover , protocols::relax::LocalRelax , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_moves::ConstrainToIdealMover , protocols::simple_moves::ScoreMover , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::stepwise::StepWiseSampleAndScreen , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::StoreCompoundTaskMover
• verbose_sampler_ : protocols::stepwise::options::StepWiseBasicOptions
• verbose_scores_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• version_ : core::chemical::ResidueDatabaseIO , core::io::rna::RDAT , core::SVNVersion , protocols::features::ResidueTypesFeatures
• verteces_ : protocols::seeded_abinitio::GrowPeptides
• vertex1_ : core::chemical::orbitals::ICoorOrbitalData
• vertex2_ : core::chemical::orbitals::ICoorOrbitalData
• vertex3_ : core::chemical::orbitals::ICoorOrbitalData
• vertex_ : core::chemical::ResidueConnection
• vertices_ : core::graph::UpperEdgeGraph< V, E > , protocols::viewer::triangle
• vertQueue : protocols::viewer::triangleIterator
• very_old_pose_ : protocols::abinitio::hConvergenceCheck , protocols::hybridization::hConvergenceCheck
• vfuncs_ : protocols::pack_daemon::DynamicAggregateFunction
• vicinity_degree_ : protocols::anchored_design::AnchoredRefineMover
• vicinity_sampling_ : protocols::anchored_design::AnchoredRefineMover
• view_ : protocols::flexpep_docking::FlexPepDockingProtocol , protocols::symmetric_docking::SymDockProtocol
• view_monte_carlo_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• virt_id_to_subunit_chain_ : core::conformation::symmetry::SymmData
• virt_id_to_subunit_num_ : core::conformation::symmetry::SymmData
• virt_id_to_subunit_residue_ : core::conformation::symmetry::SymmData
• virt_id_to_virt_num_ : core::conformation::symmetry::SymmData
• virt_num_to_virt_id_ : core::conformation::symmetry::SymmData
• virt_sugar_atr_rep_screen_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• virt_sugar_screening_pose_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• virtual_anchor_attachment_points_ : protocols::farna::setup::RNA_DeNovoParameters
• virtual_coordinates_ : core::conformation::symmetry::SymmData
• virtual_cyclic_oxygen_index_ : core::chemical::carbohydrates::CarbohydrateInfo
• virtual_res_ : protocols::hybridization::HybridizeFoldtreeDynamic , protocols::nonlocal::StarTreeBuilder
• virtual_res_list_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• 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_is_from_prior_step_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• 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
• virtualize_5prime_phosphates_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• virtualize_packable_moieties_in_screening_pose_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• visited : protocols::pockets::SmallMol
• visited_ : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• vlb_ : protocols::denovo_design::connection::BridgeChains , protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::RemodelMover
• vmax_ : protocols::noesy_assign::PeakAssignmentParameters
• vmin_ : protocols::noesy_assign::PeakAssignmentParameters
• void_mutatables : protocols::vip::VIP_Mover
• void_neighbors : protocols::vip::VIP_Mover
• vol : core::scoring::packing::SurfVol , core::scoring::packing::SurfVolDeriv , core::scoring::packstat::CavityBall
• vol_step_ : protocols::simple_moves::PeriodicBoxMover
• volume : core::scoring::packstat::CavityBallCluster , protocols::simple_moves::ThermodynamicData
• volume_ : core::scoring::FACTSRsdTypeInfo , protocols::noesy_assign::CrossPeak
• vrt_id_ : protocols::topology_broker::DensityScoringClaimer
• vrt_label_ : protocols::environment::claims::VirtResClaim
• vvr_hotspots : protocols::motif_grafting::movers::motif2scaffold_data