- v -

• v : core::kinematics::Stub , core::optimization::EItem
• V : core::scoring::electron_density::ElectronDensity
• v_ : core::optimization::Particle
• v_max_ : core::optimization::ParticleSwarmMinimizer
• v_opt : protocols::hybridization::TMalign
• val : protocols::hybridization::TMalign
• 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_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::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vall_is_chainbreak_ : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vall_makes_canonical_base_pair_ : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vall_memory_usage_ : protocols::forge::components::VarLengthBuild
• vall_name_ : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vall_non_main_chain_sugar_coords_ : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vall_non_main_chain_sugar_coords_defined_ : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vall_secstruct_ : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vall_sequence_ : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vall_size_ : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vall_torsions_ : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• vallResidueIndex_ : protocols::frag_picker::FragmentCandidate
• value : core::io::pdb::Field , core::pose::RemarkInfo , protocols::swa::rna::Torsion_Info
• value_ : core::io::silent::SilentEnergy , core::pack::dunbrack::BBDepScoreInterpData , protocols::filters::ContingentFilter , protocols::qsar::qsarPoint , protocols::wum::find_SilentStructOPs
• value_set_ : protocols::pack_daemon::InSetExpression
• values_ : protocols::filters::IfThenFilter , protocols::filters::CalculatorFilter
• vanilla_options_ : protocols::abinitio::IterativeBase , protocols::jd2::BatchJobInputter
• 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_types_ : core::chemical::ResidueType
• variant_types_list_ : core::pose::MiniPose
• variants_ : core::chemical::Selector_VARIANT_TYPE , core::chemical::Selector_MATCH_VARIANTS
• various_length_poses_ : protocols::simple_moves::GunnCost
• VARS : protocols::sparta::GDB
• vars_ : protocols::pack_daemon::VariableVectorExpression
• VARS_str : protocols::sparta::GDB
• VarsNumber : protocols::sparta::GDB
• vary_bond_angles_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• vary_bond_geometry_ : protocols::rna::RNA_DeNovoProtocol , protocols::rna::RNA_Minimizer
• vary_ca_bond_angles_ : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• vary_cutpoints_ : protocols::anchored_design::AnchoredDesignMover
• vbpos_ : protocols::motifs::MotifHit
• VDW_align_res : protocols::swa::rna::VDW_RepScreeninfo
• VDW_atr_rep_screen_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler
• vdw_calculation_annotated_sequence_ : core::scoring::rna::RNA_ScoringInfo
• vdw_delta_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• VDW_ignore_res : protocols::swa::rna::VDW_RepScreeninfo
• vdw_params : protocols::relax::CentroidRelax::parameters
• VDW_pose : protocols::swa::rna::VDW_RepScreeninfo
• VDW_RAD : protocols::sparta::PDB
• VDW_rep_alignment_RMSD_CUTOFF_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• VDW_rep_ignore_matching_res_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• VDW_rep_screen_info_ : protocols::swa::rna::StepWiseRNA_Clusterer
• VDW_rep_screen_info_list_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• VDW_rep_screen_with_physical_pose_verbose_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• vdw_scale_factor_ : core::scoring::methods::VDW_Energy , core::scoring::rna::RNA_FA_Stack , core::scoring::rna::RNA_VDW_Energy , protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• vdw_score_type_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• VDW_screen_bin_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• VDW_weight_ : protocols::anchored_design::AnchorMoversData
• 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
• vec_exclude_residues_changed_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• vec_exclude_residues_exists_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• vec_filename_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcs2::PcsEnergyParameter
• vec_filename_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• vec_individual_weight_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcs2::PcsEnergyParameter
• vec_individual_weight_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• vecAB : protocols::surface_docking::SurfaceParameters
• vecAC : protocols::surface_docking::SurfaceParameters
• vector1_loopsop_having_cdr_ : protocols::antibody2::AntibodyInfo
• vector_angle_cutoff_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• vector_dist_cutoff_ : protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• 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
• velocity : protocols::cartesian::CartesianAtom
• verbose_ : core::scoring::rna::RNA_TorsionPotential , protocols::swa::protein::StepWiseProteinCCD_Closer , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::dna::DNATorsionPotential , core::scoring::methods::LK_CosThetaEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , protocols::rna::RNA_LoopCloser , protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential , core::scoring::rna::RNA_LJ_BaseEnergy , protocols::rna::MultipleDomainMover , protocols::flxbb::InterlockAroma , protocols::simple_filters::ShapeComplementarityFilter , protocols::flxbb::LayerDesignOperation , protocols::analysis::PackStatMover , protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::rna::RNA_HelixAssembler , protocols::rna::RNA_Minimizer , protocols::simple_moves::ScoreMover , protocols::swa::rna::RNA_AnalyticLoopCloser , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::SlicedPoseJobParameters , core::scoring::rna::RNA_Mg_Energy , protocols::swa::rna::StepWiseRNA_RotamerGenerator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::task_operations::SelectBySASAOperation , core::scoring::geometric_solvation::GeometricSolEnergy , core::scoring::dna::DNATorsionEnergy , protocols::swa::protein::StepWiseProteinPoseSetup , protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper , protocols::swa::rna::StepWiseRNA_Clusterer
• version : protocols::hybridization::TMalign
• version_ : protocols::features::ResidueTypesFeatures , core::chemical::ResidueDatabaseIO
• verteces_ : protocols::seeded_abinitio::GrowPeptides
• vertices_ : protocols::viewer::triangle , core::graph::UpperEdgeGraph< V, E >
• vertQueue : protocols::viewer::triangleIterator
• very_old_pose_ : protocols::hybridization::hConvergenceCheck , protocols::abinitio::hConvergenceCheck
• vfuncs_ : protocols::pack_daemon::DynamicAggregateFunction
• vicinity_degree_ : protocols::anchored_design::AnchoredRefineMover
• vicinity_sampling_ : protocols::anchored_design::AnchoredRefineMover
• view_ : protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::symmetric_docking::SymDockProtocol
• view_monte_carlo_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• viol_level_ : protocols::constraints_additional::ConstraintEvaluator
• 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
• virtual_anchor_attachment_points_ : protocols::rna::RNA_StructureParameters
• virtual_coordinates_ : core::conformation::symmetry::SymmData
• virtual_res_ : protocols::hybridization::HybridizeFoldtreeDynamic , protocols::nonlocal::StarTreeBuilder
• virtual_res_list_ : protocols::swa::rna::StepWiseRNA_PoseSetup , protocols::swa::StepWisePoseSetup
• virtualize_5prime_phosphates_ : protocols::swa::StepWisePoseSetup
• visited_ : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• vlb_ : 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
• volume : core::scoring::packstat::CavityBallCluster
• volume_ : protocols::noesy_assign::CrossPeak , core::scoring::FACTSResidueInfo
• vrt_id_ : protocols::topology_broker::DensityScoringClaimer