Here is a list of all class members with links to the classes they belong to:

- v -

• V : protocols::sic_dock::Rose
• v_begin() : protocols::loops::Loops
• v_end() : protocols::loops::Loops
• v_indexes : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• val : protocols::hybridization::TMalign
• valid() : protocols::fldsgn::topology::DimerPairing , protocols::jd2::archive::Batch , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover , protocols::simple_moves::ExtendedPoseMover
• valid_ : protocols::fldsgn::topology::DimerPairing
• valid_anchors() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_basestep_start() : protocols::dna::DNAParameters
• valid_chain_bounds_ : protocols::flexpep_docking::FlexPepDockingFlags
• valid_chain_info() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_loop_file_keys_ : protocols::loops::JSONFormattedLoopsFileReader
• valid_peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_peptide_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• valid_receptor_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_receptor_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• valid_ref_start_struct() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_ref_start_struct_ : protocols::flexpep_docking::FlexPepDockingFlags
• valid_segments_ : protocols::backrub::BackrubSidechainMover
• valid_ss() : protocols::simple_moves::ClassicFragmentMover
• valid_surface_pose() : protocols::surface_docking::SurfaceDockingProtocol
• valid_variable_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• validate() : protocols::environment::claims::JumpClaim
• validate_downstream_orientation_atoms() : protocols::match::MatcherTask
• validate_ramachandran_hash() : protocols::features::BetaTurnDetection
• validate_template() : protocols::hybridization::HybridizeProtocol
• vall_edge_is_base_pairing_ : protocols::farna::FullAtomRNA_Fragments
• vall_is_chainbreak_ : protocols::farna::FullAtomRNA_Fragments
• vall_makes_canonical_base_pair_ : protocols::farna::FullAtomRNA_Fragments
• vall_memory_usage() : protocols::forge::components::VarLengthBuild
• vall_memory_usage_ : protocols::forge::components::VarLengthBuild
• vall_name_ : protocols::farna::FullAtomRNA_Fragments
• vall_non_main_chain_sugar_coords_ : protocols::farna::FullAtomRNA_Fragments
• vall_non_main_chain_sugar_coords_defined_ : protocols::farna::FullAtomRNA_Fragments
• vall_secstruct_ : protocols::farna::FullAtomRNA_Fragments
• vall_sequence_ : protocols::farna::FullAtomRNA_Fragments
• vall_size_ : protocols::farna::FullAtomRNA_Fragments
• vall_torsions_ : protocols::farna::FullAtomRNA_Fragments
• VallChunk() : protocols::frag_picker::VallChunk
• vallChunksFromLibraries() : protocols::frag_picker::VallProvider
• vallChunksFromLibrary() : protocols::frag_picker::VallProvider
• VallData() : protocols::frags::VallData
• VallLookbackFragMover() : protocols::simple_moves::VallLookbackFragMover
• vallNumLines() : protocols::frag_picker::VallProvider
• VallProvider() : protocols::frag_picker::VallProvider
• VallResidue() : protocols::frag_picker::VallResidue
• vallResidueIndex_ : protocols::frag_picker::FragmentCandidate
• value : protocols::stepwise::modeler::rna::Torsion_Info , protocols::stepwise::sampler::StepWiseSamplerOneValue
• value_ : protocols::filters::ContingentFilter , protocols::qsar::qsarPoint , protocols::wum::find_SilentStructOPs
• value_list_cached_ : protocols::stepwise::sampler::StepWiseSamplerOneValueComb
• value_passes() : protocols::enzdes::ValueEvaluator
• value_range() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• value_range_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• value_set() : protocols::pack_daemon::InSetExpression
• value_set_ : protocols::pack_daemon::InSetExpression
• value_type : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• value_type_ : protocols::simple_moves::AddJobPairData
• ValueEvaluator() : protocols::enzdes::ValueEvaluator
• values : protocols::pack_daemon::VectorExpression
• values_ : protocols::filters::CalculatorFilter , protocols::filters::IfThenFilter , protocols::stepwise::sampler::StepWiseSamplerOneValue
• values_from_pose() : protocols::comparative_modeling::features::ResidueFeature , protocols::comparative_modeling::features::SSFeature , protocols::comparative_modeling::features::TorsionFeature
• ValueType : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::simple_moves::AddJobPairData
• vanilla_options_ : protocols::abinitio::IterativeBase , protocols::jd2::BatchJobInputter
• var_type_ : protocols::normalmode::NormalModeMultifunc
• variable_expression() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• 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
• VariableExpression : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• VariableExpressionCOP : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::IterativeVectorExpression
• VariableExpressionOP : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::IterativeVectorExpression
• VariableExpressions : protocols::pack_daemon::VariableVectorExpression
• VariableVectorExpression() : protocols::pack_daemon::VariableVectorExpression
• variance_archive_ : protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::NormalizedEvaluatedArchive
• VarianceStatisticsArchive() : protocols::jd2::archive::VarianceStatisticsArchive
• various_length_poses_ : protocols::simple_moves::GunnCost
• VarLengthBuild : protocols::fldsgn::BluePrintBDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelMover
• VarLengthBuildAP : protocols::forge::remodel::RemodelConstraintGenerator
• VarLengthBuildOP : protocols::fldsgn::BluePrintBDR , protocols::forge::remodel::RemodelMover
• VarList : protocols::sparta::GDB
• VARS : protocols::sparta::GDB
• vars_ : protocols::pack_daemon::VariableVectorExpression
• VARS_str : protocols::sparta::GDB
• VARS_str_parser() : protocols::sparta::GDB
• vars_to_dofs() : protocols::normalmode::NormalModeMultifunc
• vars_to_params() : protocols::helical_bundle::FitSimpleHelixMultiFunc
• VarsNumber : protocols::sparta::GDB
• vary_bond_angles_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• vary_bond_geometry() : protocols::farna::RNA_Minimizer , protocols::simple_moves::ConstrainToIdealMover
• vary_bond_geometry_ : protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_Minimizer
• 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_polar_hydrogen_geometry() : protocols::stepwise::options::StepWiseBasicOptions
• vary_polar_hydrogen_geometry_ : protocols::stepwise::options::StepWiseBasicOptions
• vary_rna_bond_geometry() : protocols::stepwise::options::StepWiseBasicOptions
• vary_rna_bond_geometry_ : protocols::stepwise::options::StepWiseBasicOptions
• vbpos() : protocols::motifs::MotifHit
• vbpos_ : protocols::motifs::MotifHit
• VC : protocols::sic_dock::Rose
• VCR : protocols::sic_dock::Rose
• VdRdPhi : protocols::simple_moves::BBGaussianMover
• 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_BinScreener() : protocols::stepwise::screener::VDW_BinScreener
• vdw_delta_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• 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_rep_alignment_RMSD_CUTOFF() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• 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_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() : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• VDW_rep_screen_info() : protocols::stepwise::options::StepWiseBasicOptions
• 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
• VDW_rep_screen_physical_pose_clash_dist_cutoff() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• 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_rep_screen_with_physical_pose_verbose_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• VDW_RepScreeninfo() : protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo
• vdw_scale_factor_ : 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
• VDW_weight_ : protocols::anchored_design::AnchorMoversData
• vdwcut_ : protocols::simple_moves::CombinePoseMover
• VdwGrid() : protocols::qsar::scoring_grid::VdwGrid
• vdWpen : protocols::pockets::PocketExemplarMultifunc
• Vec : protocols::sic_dock::RigidScore , protocols::sic_dock::SICFast
• Vec1Hash : protocols::pack_daemon::PackDaemon
• 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_ex1_ : protocols::pack_daemon::VectorFunction2
• vec_ex2() : 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
• vecAB_ : protocols::surface_docking::SurfaceParameters
• vecAC() : protocols::surface_docking::SurfaceParameters
• vecAC_ : protocols::surface_docking::SurfaceParameters
• VecInt : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet
• VecIR : protocols::sic_dock::scores::MotifHashRigidScore
• vecQueue : protocols::viewer::triangleIterator
• VecReal : protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet
• Vecs : protocols::sic_dock::RigidScore
• VecSize : protocols::fldsgn::MatchResidues , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::StrandPairingSet
• VecTaskOP : protocols::flxbb::CombinedTaskOperation
• Vector : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::Helix , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::Loop , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SS_Base , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::hotspot_hashing::StubGenerator , protocols::match::Bool3DGrid , protocols::match::Bool3DGridKinemageWriter , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::TargetRotamerCoords , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::OccupiedSpaceHash , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamBuilder , protocols::match::upstream::UpstreamResTypeGeometry , protocols::match::VoxelSetIterator , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::MinimalRotamer , protocols::toolbox::match_enzdes_util::LigandConformer
• vector1_loopsop_having_cdr_ : protocols::antibody::AntibodyInfo
• vector_angle_cut() : protocols::simple_filters::DomainInterfaceFilter
• vector_angle_cut_ : protocols::simple_filters::DomainInterfaceFilter
• vector_angle_cutoff() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• vector_angle_cutoff_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• vector_dist_cut() : protocols::simple_filters::DomainInterfaceFilter
• vector_dist_cut_ : protocols::simple_filters::DomainInterfaceFilter
• vector_dist_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_expression_map_ : protocols::pack_daemon::DynamicAggregateFunction
• vector_values() : protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VectorExpression
• vector_variable_names_dec_line_ : protocols::pack_daemon::DynamicAggregateFunction
• 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
• VectorPoseMover() : protocols::moves::VectorPoseMover
• VecVecSize : protocols::fldsgn::MatchResidues
• vecx : protocols::loophash::LegacyLeapIndex
• vecy : protocols::loophash::LegacyLeapIndex
• vecz : protocols::loophash::LegacyLeapIndex
• vel_ : protocols::md::MDBase
• velocity : protocols::cartesian::CartesianAtom
• VelocityVerlet_Integrator() : protocols::md::CartesianMD
• verbose() : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::StepWiseSampleAndScreen , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::StoreCompoundTaskMover
• verbose_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc , protocols::farna::MultipleDomainMover , protocols::farna::RNA_LoopCloser , protocols::farna::RNA_Minimizer , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::rbsegment_relax::SequenceShiftMover , 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::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_scores() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• verbose_scores_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• verify() : protocols::environment::ProtectedConformation
• verify_against() : protocols::loops::Loops
• verify_backbone() : protocols::environment::ProtectedConformation
• verify_jump() : protocols::environment::ProtectedConformation
• 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() : protocols::features::ProteinSilentReport , protocols::features::Report , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , 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
• version_ : protocols::features::ResidueTypesFeatures
• verteces_ : protocols::seeded_abinitio::GrowPeptides
• vertices_ : protocols::viewer::triangle
• vertQueue : protocols::viewer::triangleIterator
• very_far_away() : protocols::simple_moves::symmetry::SymmetrySlider
• 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
• VicinityPerturber() : protocols::kinematic_closure::perturbers::VicinityPerturber
• VicinitySamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• view() : protocols::flexpep_docking::FlexPepDockingProtocol
• view_ : protocols::flexpep_docking::FlexPepDockingProtocol , protocols::symmetric_docking::SymDockProtocol
• view_constraints_in_pymol() : protocols::metal_interface::AddZincSiteConstraints
• view_monte_carlo_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• VIP_Mover() : protocols::vip::VIP_Mover
• VIP_Report() : protocols::vip::VIP_Report
• virt_sugar_atr_rep_screen_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• virt_sugar_screening_pose_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• VirtResClaim() : protocols::environment::claims::VirtResClaim
• virtual_anchor_attachment_points_ : protocols::farna::RNA_StructureParameters
• 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_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_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_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_sugar_legacy_mode_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• virtualize_5prime_phosphates_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• 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_packable_moieties_in_screening_pose_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• virtualize_sugar_and_backbone_at_moving_res() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• 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() : protocols::sic_dock::CBScoreVisitor , protocols::sic_dock::CorrectionVisitor , protocols::simple_moves::TailsScoreMover
• visited : protocols::pockets::SmallMol
• visited_ : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• VisualizeEmbeddingMover() : protocols::membrane::visualize::VisualizeEmbeddingMover
• VisualizeMembraneMover() : protocols::membrane::visualize::VisualizeMembraneMover
• vlb() : protocols::forge::remodel::RemodelConstraintGenerator
• VLB() : protocols::protein_interface_design::movers::VLB
• vlb_ : protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::RemodelMover
• VMatrix : protocols::simple_moves::BBGaussianMover
• VMax() : protocols::pack_daemon::VMax
• vmax_ : protocols::noesy_assign::PeakAssignmentParameters
• VMaxBy() : protocols::pack_daemon::VMaxBy
• VMin() : protocols::pack_daemon::VMin
• vmin_ : protocols::noesy_assign::PeakAssignmentParameters
• VMinBy() : protocols::pack_daemon::VMinBy
• void_mutatables : protocols::vip::VIP_Mover
• void_neighbors : protocols::vip::VIP_Mover
• volume() : protocols::noesy_assign::CrossPeak
• volume_ : protocols::noesy_assign::CrossPeak
• VoxelSetIterator() : protocols::match::VoxelSetIterator
• vrt_id_ : protocols::topology_broker::DensityScoringClaimer
• vrt_label() : protocols::environment::claims::VirtResClaim
• vrt_label_ : protocols::environment::claims::VirtResClaim
• vvr_hotspots : protocols::motif_grafting::movers::motif2scaffold_data