- v -

• v_begin() : protocols::loops::Loops
• v_end() : protocols::loops::Loops
• valid() : protocols::fldsgn::topology::DimerPairing , protocols::jd2::archive::Batch , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover , protocols::simple_moves::ExtendedPoseMover
• valid_anchors() : protocols::flexpep_docking::FlexPepDockingFlags
• valid_basestep_start() : protocols::dna::DNAParameters
• valid_chain_info() : protocols::flexpep_docking::FlexPepDockingFlags
• 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
• valid_surface_pose() : protocols::surface_docking::SurfaceDockingProtocol
• validate() : protocols::environment::claims::JumpClaim
• validate_downstream_orientation_atoms() : protocols::match::MatcherTask
• validate_ramachandran_hash() : protocols::features::BetaTurnDetection
• validate_template() : protocols::hybridization::HybridizeProtocol
• 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
• vallNumLines() : protocols::frag_picker::VallProvider
• VallProvider() : protocols::frag_picker::VallProvider
• VallResidue() : protocols::frag_picker::VallResidue
• value() : protocols::stepwise::sampler::StepWiseSamplerOneValue
• value_passes() : protocols::enzdes::ValueEvaluator
• value_range() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• value_set() : protocols::pack_daemon::InSetExpression
• ValueEvaluator() : protocols::enzdes::ValueEvaluator
• 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
• VarLengthBuild() : protocols::forge::components::VarLengthBuild
• VARS_str_parser() : protocols::sparta::GDB
• vars_to_dofs() : protocols::normalmode::NormalModeMultifunc
• vars_to_params() : protocols::helical_bundle::FitSimpleHelixMultiFunc
• vary_bond_geometry() : protocols::farna::RNA_Minimizer , protocols::simple_moves::ConstrainToIdealMover
• vary_polar_hydrogen_geometry() : protocols::stepwise::options::StepWiseBasicOptions
• vary_rna_bond_geometry() : protocols::stepwise::options::StepWiseBasicOptions
• vbpos() : protocols::motifs::MotifHit
• VDW_BinScreener() : protocols::stepwise::screener::VDW_BinScreener
• 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_info() : protocols::stepwise::options::StepWiseBasicOptions
• 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() : protocols::stepwise::modeler::rna::checker::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
• vecAB() : protocols::surface_docking::SurfaceParameters
• vecAC() : protocols::surface_docking::SurfaceParameters
• vector_angle_cut() : protocols::simple_filters::DomainInterfaceFilter
• vector_angle_cutoff() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• vector_dist_cut() : protocols::simple_filters::DomainInterfaceFilter
• vector_dist_cutoff() : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation
• 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
• VectorPoseMover() : protocols::moves::VectorPoseMover
• 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_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
• very_far_away() : protocols::simple_moves::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
• VIP_Mover() : protocols::vip::VIP_Mover
• VIP_Report() : protocols::vip::VIP_Report
• VirtResClaim() : protocols::environment::claims::VirtResClaim
• virtual_sugar_do_minimize() : 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
• virtualize_distal_partition() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• 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
• visit() : protocols::sic_dock::CBScoreVisitor , protocols::sic_dock::CorrectionVisitor , protocols::simple_moves::TailsScoreMover
• VisualizeEmbeddingMover() : protocols::membrane::visualize::VisualizeEmbeddingMover
• VisualizeMembraneMover() : protocols::membrane::visualize::VisualizeMembraneMover
• 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
• VoxelSetIterator() : protocols::match::VoxelSetIterator
• vrt_label() : protocols::environment::claims::VirtResClaim