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

- v -

• v : core::kinematics::Stub , core::optimization::EItem
• V : core::scoring::electron_density::ElectronDensity , protocols::sic_dock::Rose
• V2000 : core::chemical::sdf::MolWriter
• V3000 : core::chemical::sdf::MolWriter
• v_ : core::optimization::Particle
• V_ : protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup
• v_angle_baseline : core::scoring::magnesium::MgEnergy
• v_angle_width() : core::scoring::magnesium::MgKnowledgeBasedPotential
• v_angle_width2_ : core::scoring::magnesium::MgEnergy
• v_angle_width_ : core::scoring::magnesium::MgEnergy , core::scoring::magnesium::MgKnowledgeBasedPotential
• v_begin() : protocols::loops::Loops
• v_end() : protocols::loops::Loops
• v_indexes : protocols::motif_grafting::movers::motif2scaffold_data , protocols::motif_grafting::movers::MotifMatch
• v_max_ : core::optimization::ParticleSwarmMinimizer
• val : protocols::hybridization::TMalign
• valence_electrons_p() : core::chemical::ElectronConfiguration
• valence_electrons_s() : core::chemical::ElectronConfiguration
• valence_electrons_sp() : core::chemical::ElectronConfiguration
• valence_electrons_sp_ : core::chemical::ElectronConfiguration
• valence_electrons_spd() : core::chemical::ElectronConfiguration
• valence_electrons_spd_ : core::chemical::ElectronConfiguration
• valence_quantum_number_ : core::chemical::ElectronConfiguration
• valid : core::fragment::picking_old::concepts::Extent< PageIterator > , core::graph::ArrayPoolElement< T > , core::graph::EdgeListConstIterator , core::graph::EdgeListIterator , core::id::AtomID , core::id::DOF_ID , core::id::JumpID , core::id::NamedAtomID , core::id::NamedStubID , core::id::StubID , core::id::TorsionID , core::kinematics::Edge , core::scoring::DimerPairing , core::scoring::sc::_RESULTS , protocols::fldsgn::topology::DimerPairing , protocols::jd2::archive::Batch , protocols::nonlocal::Chunk , protocols::nonlocal::SingleFragmentMover , protocols::simple_moves::ExtendedPoseMover
• valid_ : core::fragment::FragData , core::scoring::DimerPairing , 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_dssp_codes_ : protocols::sewing::sampling::requirements::SegmentDsspRequirement
• valid_ends() : core::scoring::dssp::StrandPairing
• 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_ss_stub_abego_match() : core::indexed_structure_store::ABEGOHashedFragmentStore
• valid_surface_pose() : protocols::surface_docking::SurfaceDockingProtocol
• valid_variable_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• validate() : protocols::environment::claims::JumpClaim
• validate_bundle() : protocols::features::helixAssembly::HelixBundleFeatures
• validate_downstream_orientation_atoms() : protocols::match::MatcherTask
• validate_dunbrack_binary() : core::pack::dunbrack::RotamerLibrary
• validate_input() : core::sequence::Aligner
• validate_ramachandran_hash() : protocols::features::BetaTurnDetection
• validate_template() : protocols::hybridization::HybridizeProtocol
• 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_key_ : protocols::frag_picker::VallChunk
• vall_keys_ : protocols::frag_picker::VallProvider
• vall_last_residue_key_ : protocols::frag_picker::VallProvider
• VALL_LOOKBACK_DATA : core::pose::datacache::CacheableDataType
• vall_makes_canonical_base_pair_ : protocols::farna::fragments::FullAtomRNA_Fragments
• vall_memory_usage() : protocols::forge::components::VarLengthBuild
• 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
• vall_torsions_file() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• 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 , core::fragment::picking_old::vall::VallLibrarian
• VallFragmentEvalCOP : core::fragment::picking_old::vall::VallLibrarian
• VallFragmentEvalOP : core::fragment::picking_old::vall::VallLibrarian
• VallFragmentEvalOPs : core::fragment::picking_old::vall::VallLibrarian
• VallFragmentGen() : core::fragment::picking_old::vall::gen::VallFragmentGen
• VallFragmentGenCOP : core::fragment::picking_old::vall::VallLibrarian
• VallFragmentGenOP : core::fragment::picking_old::vall::VallLibrarian
• VallFragmentGenOPs : core::fragment::picking_old::vall::VallLibrarian
• VallFragmentScore : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::scores::VallFragmentScore , core::fragment::picking_old::vall::VallLibrarian
• 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
• VallResidueConstIterator : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::scores::VallFragmentScore , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallSection
• vallResidueIndex_ : protocols::frag_picker::FragmentCandidate
• VallResidueIterator : core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallSection
• VallSectionConstIterator : core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallLibrary
• VallSectionIterator : core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallLibrary
• Value : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T >
• value : core::io::pdb::Field , core::io::RemarkInfo , core::io::silent::SilentEnergy , core::scoring::hbonds::FadeInterval , core::scoring::rna::data::RNA_Reactivity , protocols::stepwise::modeler::rna::Torsion_Info , protocols::stepwise::sampler::StepWiseSamplerOneValue
• value_ : core::io::silent::SilentEnergy , core::scoring::rna::data::RNA_Reactivity , protocols::filters::ContingentFilter , protocols::qsar::qsarPoint , protocols::wum::find_SilentStructOPs
• value_deriv() : core::scoring::hbonds::FadeInterval
• 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 : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::import_pose::atom_tree_diffs::ScoreLessThanComparator , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• value_type_ : core::scoring::methods::SplitUnfoldedTwoBodyEnergy , 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_for_aa() : core::sequence::MatrixScoringScheme
• values_from_pose() : protocols::comparative_modeling::features::ResidueFeature , protocols::comparative_modeling::features::SSFeature , protocols::comparative_modeling::features::TorsionFeature
• ValueType : core::fragment::FragCache< T > , core::fragment::FragStore< T > , 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
• variant_ : core::chemical::DeleteVariantType
• variant_exceptions() : core::chemical::ResidueTypeFinder
• variant_exceptions_ : core::chemical::ResidueTypeFinder
• variant_type_enums() : core::chemical::ResidueType
• variant_type_status_ : core::chemical::ResidueProperties
• variant_types() : core::chemical::ResidueType , core::pose::MiniPose
• variant_types_list() : core::pose::MiniPose
• variant_types_list_ : core::pose::MiniPose
• variants() : core::chemical::ResidueTypeFinder
• variants_ : core::chemical::Selector_MATCH_VARIANTS , core::chemical::Selector_VARIANT_TYPE
• variants_in_sets() : core::chemical::ResidueTypeFinder
• variants_in_sets_ : core::chemical::ResidueTypeFinder
• 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_index_to_torsion_id_ : protocols::ncbb::SecStructMinimizeMultiFunc
• VARS_str : protocols::sparta::GDB
• VARS_str_parser() : protocols::sparta::GDB
• vars_to_dofs() : protocols::ncbb::SecStructMinimizeMultiFunc , 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::options::RNA_MinimizerOptions , protocols::simple_moves::ConstrainToIdealMover
• 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_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_polar_hydrogen_geometry_ : protocols::stepwise::options::StepWiseBasicOptions
• vary_rna_bond_geometry() : protocols::stepwise::options::StepWiseBasicOptions
• vary_rna_bond_geometry_ : protocols::stepwise::options::StepWiseBasicOptions
• vary_stepsize() : protocols::docking::SlideIntoContact , protocols::rigid::RigidBodyTransMover
• vary_stepsize_ : protocols::docking::SlideIntoContact , protocols::rigid::RigidBodyTransMover
• VaryLoopLengthMover() : protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover
• vbpos() : protocols::motifs::MotifHit
• vbpos_ : protocols::motifs::MotifHit
• VC : protocols::sic_dock::Rose
• VCR : protocols::sic_dock::Rose
• vd_ : core::chemical::ICoorAtomID
• vd_to_index_ : core::chemical::ResidueType
• VdRdPhi : protocols::simple_moves::BBGaussianMover
• vdw_ : core::scoring::vdwaals::VDWTrieEvaluator
• VDW_align_res : protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• vdw_atom_list() : core::scoring::rna::RNA_AtomVDW
• 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_CachedRepScreenInfo() : protocols::stepwise::modeler::rna::checker::VDW_CachedRepScreenInfo
• vdw_calculation_annotated_sequence() : core::scoring::rna::RNA_ScoringInfo
• vdw_calculation_annotated_sequence_ : core::scoring::rna::RNA_ScoringInfo
• vdw_delta_ : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• vdw_depth_ : core::scoring::VdWTinkerPotential
• VDW_Energy() : core::scoring::vdwaals::VDW_Energy
• VDW_Grid() : protocols::stepwise::modeler::rna::checker::VDW_Grid
• 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
• 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 : core::pose::datacache::CacheableDataType
• 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::VDW_CachedRepScreenInfo
• 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_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_ : 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::VDW_CachedRepScreenInfo
• 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_type_ : core::scoring::VdWTinkerResidueInfo
• vdw_weight() : core::scoring::vdwaals::VDWTrieEvaluator
• vdw_weight_ : core::scoring::vdwaals::VDWTrieEvaluator
• VDW_weight_ : protocols::anchored_design::AnchorMoversData
• VDWaalsRadius : core::chemical::Element
• VdWaalsRadiusCSD : core::chemical::gasteiger::GasteigerAtomTypeData
• VDWAtom() : core::scoring::vdwaals::VDWAtom
• vdwcut_ : protocols::simple_moves::CombinePoseMover
• VdwGrid() : protocols::qsar::scoring_grid::VdwGrid
• vdWpen : protocols::pockets::PocketExemplarMultifunc
• VDWTINKER_POSE_INFO : core::pose::datacache::CacheableDataType
• VdWTinkerEnergy() : core::scoring::methods::VdWTinkerEnergy
• VdWTinkerPoseInfo() : core::scoring::VdWTinkerPoseInfo
• VdWTinkerPotential() : core::scoring::VdWTinkerPotential
• VdWTinkerResidueInfo() : core::scoring::VdWTinkerResidueInfo
• VdWTinkerResPairMinData() : core::scoring::methods::VdWTinkerResPairMinData
• VdWTinkerRotamerSetInfo() : core::scoring::VdWTinkerRotamerSetInfo
• VDWTrieCountPair1B() : core::scoring::vdwaals::VDWTrieCountPair1B
• VDWTrieEvaluator() : core::scoring::vdwaals::VDWTrieEvaluator
• Vec : protocols::sic_dock::RigidScore , protocols::sic_dock::SICFast
• Vec1Hash : protocols::pack_daemon::PackDaemon
• Vec3 : core::scoring::sc::MolecularSurfaceCalculator
• 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 : core::conformation::symmetry::SymmData , core::kinematics::Jump , core::kinematics::RT , core::kinematics::Stub , core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleParameter , core::scoring::VdWTinkerResidueInfo , 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() : core::select::residue_selector::InterGroupInterfaceByVectorSelector , protocols::simple_filters::DomainInterfaceFilter
• 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_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_cut_ : core::select::residue_selector::InterGroupInterfaceByVectorSelector , 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
• Vectors : core::scoring::lkball::LK_BallEnergy , core::scoring::lkball::LKB_ResidueInfo
• 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::farna::options::RNA_BasicOptions , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::magnesium::MgHydrater , 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_ : 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_sampler_ : protocols::stepwise::options::StepWiseBasicOptions
• 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_bb_bins() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• verify_chain_setup() : core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator
• verify_jump() : protocols::environment::ProtectedConformation
• verify_omgphipsi_bins() : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• verify_parameters_() : core::scoring::func::MixtureFunc
• verify_patch_areas_correct() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• verify_phipsi_bins() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• 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() : core::io::rna::RDAT , core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::SurfaceEnergy , core::scoring::aa_composition_energy::AACompositionEnergy , core::scoring::aa_repeat_energy::AARepeatEnergy , core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::cryst::XtalMLEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::lkball::LK_BallEnergy , core::scoring::loop_graph::LoopCloseEnergy , core::scoring::magnesium::MgEnergy , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPEnvEnergy , core::scoring::membrane::FaMPEnvSmoothEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPCbetaEnergy , core::scoring::membrane::MPEnvEnergy , core::scoring::membrane::MPLipoEnergy , core::scoring::membrane::MPNonHelixPenalty , core::scoring::membrane::MPPairEnergy , core::scoring::membrane::MPTerminiPenalty , core::scoring::membrane::MPTMProjPenalty , core::scoring::methods::BurialEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenPairMotifDegreeEnergy , core::scoring::methods::CenPairMotifEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::D2H_SA_Energy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::DNA_EnvPairEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::FreeDOF_Energy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::IntermolEnergy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MissingEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OtherPoseEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::P_AA_ss_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RingClosureEnergy , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SplitUnfoldedTwoBodyEnergy , core::scoring::methods::SSElementMotifContactEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::nv::NVscore , core::scoring::orbitals::OrbitalsScore , core::scoring::packing::HolesEnergy , core::scoring::packing::HolesEnergyRes , core::scoring::packing::SurfEnergy , core::scoring::packing::SurfVolEnergy , core::scoring::rna::chemical_shift::RNA_ChemicalShiftEnergy , core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RG_Energy_RNA , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::saxs::FastSAXSEnergy , core::scoring::saxs::SAXSEnergy , core::scoring::saxs::SAXSEnergyCreatorCEN , core::scoring::saxs::SAXSEnergyCreatorFA , core::scoring::sym_e::symEnergy , core::scoring::vdwaals::VDW_Energy , core::SVNVersion , 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_ : core::chemical::ResidueDatabaseIO , core::io::rna::RDAT , core::SVNVersion , protocols::features::ResidueTypesFeatures
• verteces_ : protocols::seeded_abinitio::GrowPeptides
• vertex() : core::chemical::ICoorAtomID , core::chemical::ResidueConnection
• vertex1() : core::chemical::orbitals::ICoorOrbitalData
• vertex1_ : core::chemical::orbitals::ICoorOrbitalData
• vertex2() : core::chemical::orbitals::ICoorOrbitalData
• vertex2_ : core::chemical::orbitals::ICoorOrbitalData
• vertex3() : core::chemical::orbitals::ICoorOrbitalData
• vertex3_ : core::chemical::orbitals::ICoorOrbitalData
• vertex_ : core::chemical::ResidueConnection
• vertex_already_reached() : core::pack::interaction_graph::InteractionGraphBase
• VertexClass : core::graph::UEEdge< V, E > , core::graph::UEVertex< V, E > , core::graph::UpperEdgeGraph< V, E >
• VertexVector : core::graph::UpperEdgeGraph< V, E >
• vertices_ : core::graph::UpperEdgeGraph< V, E > , 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
• violates() : protocols::sewing::sampling::requirements::GlobalLengthRequirement , protocols::sewing::sampling::requirements::GlobalRequirement , protocols::sewing::sampling::requirements::IntraSegmentRequirement , protocols::sewing::sampling::requirements::RequirementSet , protocols::sewing::sampling::requirements::ResidueRetentionRequirement , protocols::sewing::sampling::requirements::SegmentDsspRequirement , protocols::sewing::sampling::requirements::SegmentLengthRequirement
• viols() : core::scoring::func::CountViolFunc , core::scoring::func::SkipViolFunc
• VIP_Mover() : protocols::vip::VIP_Mover
• VIP_Report() : protocols::vip::VIP_Report
• 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
• VirtResClaim() : protocols::environment::claims::VirtResClaim
• virtual_anchor_attachment_points() : protocols::farna::setup::RNA_DeNovoParameters
• virtual_anchor_attachment_points_ : protocols::farna::setup::RNA_DeNovoParameters
• virtual_coordinates_ : core::conformation::symmetry::SymmData
• virtual_cyclic_oxygen_index() : core::chemical::carbohydrates::CarbohydrateInfo
• 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_sidechain() : core::pack::rotamers::SingleResidueRotamerLibrary
• 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
• VirtualCoordinate() : core::conformation::symmetry::VirtualCoordinate
• 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() : core::conformation::AddEdgeVisitor< Vertex, Edge > , core::environment::FoldTreeSketch , protocols::sic_dock::CBScoreVisitor , protocols::sic_dock::CorrectionVisitor , protocols::simple_moves::TailsScoreMover
• visited() : core::environment::FoldTreeSketch::Node , 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::denovo_design::connection::BridgeChains , 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
• vol : core::scoring::packing::SurfVol , core::scoring::packing::SurfVolDeriv , core::scoring::packstat::CavityBall
• vol_step_ : protocols::simple_moves::PeriodicBoxMover
• volume() : core::scoring::FACTSRsdTypeInfo , core::scoring::packstat::CavityBallCluster , protocols::cryst::Spacegroup , protocols::cryst::WallpaperGroup , protocols::noesy_assign::CrossPeak , protocols::simple_moves::ThermodynamicData
• volume_ : core::scoring::FACTSRsdTypeInfo , protocols::noesy_assign::CrossPeak
• voxel_volume() : core::scoring::electron_density::ElectronDensity
• VoxelSetIterator() : protocols::match::VoxelSetIterator
• VoxelSpacingMultifunc() : protocols::electron_density::VoxelSpacingMultifunc
• VoxelSpacingRefinementMover() : protocols::electron_density::VoxelSpacingRefinementMover
• 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