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

- w -

• w : protocols::simple_filters::Quat
• w1_ : core::scoring::func::SoedingFunc
• w2_ : core::scoring::func::SoedingFunc
• W2I_1 : protocols::sparta::ANN
• W2I_2 : protocols::sparta::ANN
• W2I_3 : protocols::sparta::ANN
• W2L1_1 : protocols::sparta::ANN
• W2L1_2 : protocols::sparta::ANN
• W2L1_3 : protocols::sparta::ANN
• W2L2_1 : protocols::sparta::ANN
• W2L2_2 : protocols::sparta::ANN
• W2L2_3 : protocols::sparta::ANN
• wait_for_go_signal() : protocols::jd2::MPIWorkPoolJobDistributor
• wait_for_remote_vars() : protocols::optimize_weights::OptEMultifunc
• wait_semaphore() : protocols::boinc::Boinc
• waiting_on_dependencies() : protocols::forge::build::BuildInstruction
• WalkingBondAnglePerturber() : protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber
• WalkingPerturber() : protocols::kinematic_closure::perturbers::WalkingPerturber
• wall_time() : protocols::wum::MPI_WorkUnitManager
• wallpaper_group() : protocols::cryst::MakeLayerMover
• WallpaperGroup() : protocols::cryst::WallpaperGroup
• was_modified() : protocols::frag_picker::scores::FragmentScoreMap
• was_modified_ : protocols::frag_picker::scores::FragmentScoreMap
• was_successful() : protocols::loop_modeling::LoopMover
• was_successful_ : protocols::loop_modeling::LoopMover
• water_adduct_hbond_potential_ : core::scoring::ScoringManager
• water_adduct_hbond_score() : core::scoring::WaterAdductHBondPotential
• water_builder_map_ : core::scoring::lkball::LKB_ResidueInfo
• water_dielectric() : core::scoring::methods::EnergyMethodOptions
• water_dielectric_ : core::scoring::methods::EnergyMethodOptions
• WATER_PACKING_INFO : core::pose::datacache::CacheableDataType
• WaterAdductHBondEnergy() : core::scoring::methods::WaterAdductHBondEnergy
• WaterAdductHBondPotential() : core::scoring::WaterAdductHBondPotential
• WaterAdductIntraEnergy() : core::scoring::methods::WaterAdductIntraEnergy
• WaterBuilder() : core::scoring::lkball::WaterBuilder
• WaterBuilderMap : core::scoring::lkball::LKB_ResidueInfo
• WaterFeatures() : protocols::features::WaterFeatures
• WaterFeaturesCreator() : protocols::features::WaterFeaturesCreator
• WaterPackingInfo() : core::pack::rotamer_set::WaterPackingInfo
• waters() : core::scoring::lkball::LKB_ResidueInfo , core::scoring::lkball::lkbtrie::LKBAtom
• waters_ : core::scoring::lkball::LKB_ResidueInfo , core::scoring::lkball::lkbtrie::LKBAtom
• WaterWeightGridSet() : core::scoring::geometric_solvation::WaterWeightGridSet
• wbb_bb_ : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::weight_triple
• wbb_sc_ : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::weight_triple
• wc_edge_paired() : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• wc_edge_paired_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• wdw_to_freeze_ : protocols::hybridization::CartesianSampler , protocols::hybridization::FragmentBiasAssigner
• weight() : core::chemical::Element , core::io::silent::SilentEnergy , core::scoring::AtomNeighbor , core::scoring::constraints::SequenceProfileConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::func::TopOutFunc , core::scoring::hbonds::HBond , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::packstat::PackingScore , core::scoring::RDC , core::scoring::RDC_Rohl , core::scoring::rna::data::RNA_Datum , core::scoring::sc::MolecularSurfaceCalculator , core::scoring::SmallAtNb , protocols::abinitio::PairingStatEntry , protocols::abinitio::PairingStatistics , protocols::antibody::design::CDRGraftDesignOptions , protocols::simple_moves::MSDMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::topology_broker::weights::AbinitioMoverWeight , protocols::topology_broker::weights::ConstAbinitioMoverWeight , protocols::topology_broker::weights::LargeFragWeight , protocols::topology_broker::weights::SmallFragWeight , protocols::topology_broker::weights::SmoothFragWeight
• weight_ : core::io::silent::SilentEnergy , core::scoring::AtomNeighbor , core::scoring::constraints::SequenceProfileConstraint , core::scoring::CSA , core::scoring::DC , core::scoring::electron_density::OneGaussianScattering , core::scoring::fiber_diffraction::OneGaussianScattering , core::scoring::func::CircularPowerFunc , core::scoring::func::CircularSplineFunc , core::scoring::func::CountViolFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SplineFunc , core::scoring::func::TopOutFunc , core::scoring::hbonds::HBond , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::RDC , core::scoring::RDC_Rohl , core::scoring::rna::data::RNA_Datum , core::scoring::SmallAtNb , protocols::abinitio::PairingStatEntry , protocols::cryst::SetCrystWeightMover , protocols::denovo_design::constraints::CoordinateConstraintGenerator , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::SheetConstraintGenerator , protocols::jumping::JumpSelector::JumpWeightDef , protocols::moves::MoverContainer , protocols::pockets::PocketConstraint , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::scoring::methods::pcs2::PcsDataLanthanide , protocols::scoring::methods::pcs2::PcsInputFile , protocols::scoring::methods::pcs::PCS_data_per_lanthanides , protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1 , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4 , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::MSDMover , protocols::topology_broker::weights::ConstAbinitioMoverWeight , protocols::topology_broker::weights::LargeFragWeight , protocols::topology_broker::weights::SmallFragWeight , protocols::topology_broker::weights::SmoothFragWeight
• weight_factor_ : protocols::toolbox::IGLigandDesignEdgeUpweighter , protocols::toolbox::ResidueGroupIGEdgeUpweighter
• weight_func() : core::scoring::AtomNeighbor
• weight_func_ : core::scoring::AtomNeighbor
• weight_map() : protocols::toolbox::pose_metric_calculators::EnergiesData
• weight_map_ : protocols::toolbox::pose_metric_calculators::EnergiesData
• weight_min_ : protocols::cryst::SetCrystWeightMover
• weight_scale_ : protocols::cryst::SetCrystWeightMover
• WEIGHT_Tab : protocols::sparta::Sparta::SpartaLib
• weight_type2name_ : core::scoring::hbonds::HBondTypeManager
• weight_type_from_name() : core::scoring::hbonds::HBondTypeManager
• weight_type_lookup() : core::scoring::hbonds::HBondDatabase
• weight_type_lookup_ : core::scoring::hbonds::HBondDatabase
• weighted_atom_pair_energy() : core::scoring::vdwaals::VDWTrieEvaluator
• weighted_average() : protocols::mpi_refinement::StructAvrgMover
• weighted_counts_ : protocols::canonical_sampling::SimulatedTempering
• weighted_energy_map() : protocols::toolbox::pose_metric_calculators::EnergiesData
• weighted_energy_map_vector() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• weighted_energy_methods_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• weighted_func() : protocols::fldsgn::SheetConstraintGenerator
• weighted_random_mover_ : protocols::carbohydrates::GlycanRelaxMover
• weighted_sampler_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• weighted_string_of() : core::scoring::EMapVector
• weighted_total() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::EnergiesData
• weighted_total_ : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• weighted_total_no_master() : protocols::toolbox::pose_metric_calculators::EnergiesData
• weighted_total_no_master_vector() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• weighted_total_vector() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• WeightedFragmentSmoothTrialMover() : protocols::hybridization::WeightedFragmentSmoothTrialMover
• WeightedFragmentTrialMover() : protocols::hybridization::WeightedFragmentTrialMover
• WeightedMethodPair : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• weightFileName : protocols::sparta::Sparta::SpartaLib
• WeightMap : protocols::jd2::archive::EvaluatedArchive
• WeightRangeConstraint() : protocols::optimize_weights::WeightRangeConstraint
• weights() : core::scoring::Energies , core::scoring::ScoreFunction
• Weights : protocols::abinitio::PairingStatistics
• weights() : protocols::jd2::archive::EvaluatedArchive , protocols::moves::MoverContainer
• weights_ : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::scoring::disulfides::Cb_Distance_Func , core::scoring::func::SOGFunc_Impl , core::scoring::func::USOGFunc , core::scoring::hbonds::HBondEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::packstat::PackingScore , core::scoring::rna::RNA_SuitePotential , core::scoring::ScoreFunction , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::canonical_sampling::SimulatedTempering , protocols::filters::IfThenFilter , protocols::frag_picker::CompareByScoreCombination , protocols::frag_picker::DiversifyCrmsdByClustering , protocols::frag_picker::DiversifyCrmsdSelector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::scores::FragmentAllAtomCrmsd , protocols::frag_picker::scores::FragmentChunkCrms , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::moves::SimulatedTempering , protocols::sic_dock::CBScore , protocols::sic_dock::JointScore , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::toolbox::DecoySetEvaluation , protocols::toolbox::task_operations::MutationSetDesignOperation
• weights_to_scan_ : protocols::electron_density::BfactorFittingMover
• well_depth() : core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc
• well_depth_ : core::scoring::func::FadeFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc
• well_depth_burial_ : core::scoring::rna::data::RNA_DataBackboneEnergy
• well_depth_exposed_ : core::scoring::rna::data::RNA_DataBackboneEnergy
• well_offset_ : core::scoring::func::FadeFunc
• wfa_atr() : protocols::match::output::MatchCollisionFilter
• wfa_atr_ : protocols::match::output::MatchCollisionFilter
• wfa_rep() : protocols::match::output::MatchCollisionFilter
• wfa_rep_ : protocols::match::output::MatchCollisionFilter
• wfa_sol() : protocols::match::output::MatchCollisionFilter
• wfa_sol_ : protocols::match::output::MatchCollisionFilter
• wg_ : protocols::cryst::MakeLayerMover
• whatIsTooSmall() : protocols::pockets::PocketGrid
• where_is_line() : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• which_ancestor_ : core::chemical::ChangeAncestory
• which_bin_i() : core::scoring::bin_transitions::BinTransitionData
• which_bin_iplus1() : core::scoring::bin_transitions::BinTransitionData
• which_chain() : protocols::fldsgn::CircularPermutation , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• which_chi_ : core::pack::task::EX
• which_component_ : core::scoring::func::MinMultiHarmonicFunc
• which_cst_being_processed_ : protocols::match::output::UpstreamHitCacher
• which_geom_cst_ : protocols::match::TaskOperationMPM
• which_jump_ : protocols::stepwise::sampler::JumpStepWiseSampler
• which_netstate_worst_top_ : core::pack::annealer::MultiCoolAnnealer
• which_node() : core::pack::interaction_graph::EdgeBase
• which_point_for_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• which_point_for_atom_ : protocols::match::upstream::UpstreamResTypeGeometry
• which_residue_alternative_set_is_moving_residue() : protocols::stepwise::modeler::StepWiseConnectionSampler
• which_scratch_res_is_cut_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• which_sheet() : protocols::fldsgn::topology::SheetSet
• which_side() : core::pose::rna::BaseStack , protocols::fldsgn::topology::Sheet
• which_side_ : core::pose::rna::BaseStack
• which_ssElement() : core::scoring::methods::SSElementMotifContactEnergy , protocols::simple_filters::SSElementMotifContactFilter
• which_top_entity() : protocols::pack_daemon::MultistateFitnessFunction
• which_torsions() : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_MultiPoseCloser , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• which_torsions_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler
• WhileMover() : protocols::moves::WhileMover
• whoami() : protocols::toolbox::GreedyKCenter , protocols::toolbox::KCluster , protocols::toolbox::KMedoid
• whole_interface_ : protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueIEFilter
• whole_line : core::scoring::packstat::SimplePDB_Atom
• whole_pose_ : protocols::enzdes::EnzScoreFilter , protocols::simple_filters::ResidueIEFilter
• whole_pose_context_enmeths_ : core::scoring::MinimizationGraph
• whole_pose_context_enmeths_begin() : core::scoring::MinimizationGraph
• whole_pose_context_enmeths_end() : core::scoring::MinimizationGraph
• whole_protein_ : protocols::simple_filters::EnergyPerResidueFilter
• whole_struct_cluster_radius_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• whole_structure_types() : core::scoring::ScoreFunction
• WholeBodyRotationMover() : protocols::rigid::WholeBodyRotationMover
• WholeBodyTranslationMover() : protocols::rigid::WholeBodyTranslationMover
• WholeStructureEnergy() : core::scoring::methods::WholeStructureEnergy
• WholeStructureMoveSet_ : protocols::rbsegment_relax::RBSegmentRelax
• WholeWholeEnergyInvoker() : core::scoring::etable::WholeWholeEnergyInvoker< Evaluator >
• WI_1 : protocols::sparta::ANN
• WI_2 : protocols::sparta::ANN
• WI_3 : protocols::sparta::ANN
• wide_move_tolerance_sqr_ : core::scoring::NeighborList
• wide_nblist_ : core::scoring::NeighborList
• wide_nblist_extension_ : core::scoring::NeighborList
• wide_reference_coords_ : core::scoring::NeighborList
• widget_name() : protocols::genetic_algorithm::EntityElementCreator , protocols::multistate_design::PosTypeCreator
• width : core::chemical::rna::GaussianParameter , core::io::silent::SilentEnergy , core::sequence::SequenceProfile
• width_ : core::io::silent::SilentEnergy , protocols::frag_picker::scores::FragmentScoreManager , protocols::membrane::visualize::VisualizeMembraneMover , protocols::qsar::scoring_grid::GridManager , protocols::viewer::ConformationViewer
• WidthFirstSlidingWindowLoopClosure() : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• wiggle_cdr_h3_ : protocols::antibody::H3RefineCCD
• wildcard_mm_bondangle_library_ : core::scoring::mm::MMBondAngleLibrary
• wildcard_mm_torsion_library_ : core::scoring::mm::MMTorsionLibrary
• WildcardMatch() : core::scoring::sc::MolecularSurfaceCalculator
• wind_down_simulation() : protocols::canonical_sampling::MetropolisHastingsMover
• window() : protocols::viewer::ConformationViewer
• WINDOW_ : core::scoring::electron_density::ElectronDensity
• window_ : protocols::cryst::LoadDensityMapMover , protocols::noesy_assign::FoldResonance
• window_acceptance_ratio_ : protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• WINDOW_SIZE : protocols::ss_prediction::SS_predictor
• window_size_ : protocols::loophash::LoopHashDiversifier
• WindowList : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• winning_address_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• winning_ranks_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer , protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• winning_tag_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• wipe() : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• wipe_out_moving_residues() : protocols::stepwise::monte_carlo::mover::DeleteMover
• wipe_two_body_energies_for_node_state() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge
• within1bonds_sets_for_atom() : core::chemical::ResidueType
• within1bonds_sets_for_atom_ : core::chemical::ResidueType
• within2bonds_sets_for_atom() : core::chemical::ResidueType
• within2bonds_sets_for_atom_ : core::chemical::ResidueType
• within_reach() : protocols::match::HitNeighborFinder
• without_my_constraints() : protocols::ligand_docking::ResidueTorsionRestraints
• WL1_1 : protocols::sparta::ANN
• WL1_2 : protocols::sparta::ANN
• WL1_3 : protocols::sparta::ANN
• WL2_1 : protocols::sparta::ANN
• WL2_2 : protocols::sparta::ANN
• WL2_3 : protocols::sparta::ANN
• WobbleMover() : protocols::simple_moves::WobbleMover
• work_dir_ : protocols::simple_filters::ExternalEvaluator
• work_unit_list() : protocols::wum::WorkUnitManager
• work_unit_list_ : protocols::wum::WorkUnitList , protocols::wum::WorkUnitManager
• worker_finish_summary() : protocols::boinc::Boinc
• worker_initialized_ : protocols::boinc::Boinc
• worker_is_finished() : protocols::boinc::Boinc
• worker_running_ : protocols::boinc::Boinc
• worker_shutdown() : protocols::boinc::Boinc
• worker_startup() : protocols::boinc::Boinc
• workers_finished() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• workers_finished_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• working_align_pose_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• working_align_res : protocols::stepwise::modeler::rna::checker::VDW_RepScreenInfo
• working_best_alignment() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_best_alignment_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_block_stack_above_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_block_stack_above_res_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_block_stack_below_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_block_stack_below_res_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_bridge_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_bridge_res_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_calc_rms_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_calc_rms_res_ : protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_denovo_scorefxn_ : protocols::farna::RNA_FragmentMonteCarlo
• working_extra_minimize_res_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• working_fixed_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_fixed_res_ : protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_floating_base_anchor_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_force_anti_chi_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_force_anti_chi_res_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_force_north_sugar_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_force_north_sugar_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_force_south_sugar_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_force_south_sugar_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_force_syn_chi_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_force_syn_chi_res_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_global_sample_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_global_sample_res_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_minimize_res() : protocols::stepwise::modeler::StepWiseMinimizer
• working_minimize_res_ : protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler
• working_model_ : protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelMover
• working_moving_partition_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_moving_partition_res_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_moving_res() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_moving_res_ : protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_moving_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_moving_res_list_ : protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_moving_suite() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_moving_suite_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_moving_suite_list() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_moving_suite_list_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_native_alignment() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_native_alignment_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_native_pose : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_native_pose_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_pack_res() : protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::StepWiseMinimizer
• working_pack_res_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::StepWiseMinimizer
• working_pack_res_was_inputted() : protocols::stepwise::modeler::packer::StepWisePacker
• working_pack_res_was_inputted_ : protocols::stepwise::modeler::packer::StepWisePacker
• working_parameters() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::StepWiseModeler
• working_parameters_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup , protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler
• working_parameters_exist_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• working_pose_ : core::scoring::rna::data::RNA_DMS_Potential
• working_pose_with_probe_ : core::scoring::rna::data::RNA_DMS_Potential
• working_prepack_res_ : protocols::stepwise::modeler::StepWiseModeler
• working_protonated_H1_adenosine_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_protonated_H1_adenosine_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_reference_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_res() : core::pose::full_model_info::FullModelInfo
• working_res_list() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_sequence() : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_sequence_ : protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• working_set_size_ : protocols::boinc::Boinc
• working_set_size_max_val_ : protocols::boinc::Boinc
• working_superimpose_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_superimpose_res_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_terminal_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_terminal_res_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• working_to_sliced_res_map_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• workingSetGen() : protocols::forge::remodel::RemodelWorkingSet
• WorkUnit_BatchRelax() : protocols::relax::WorkUnit_BatchRelax
• WorkUnit_BatchRelax_and_PostRescore() : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• WorkUnit_bbGauss() : protocols::mpi_refinement::WorkUnit_bbGauss
• WorkUnit_CombinePose() : protocols::mpi_refinement::WorkUnit_CombinePose
• WorkUnit_FragInsert() : protocols::mpi_refinement::WorkUnit_FragInsert
• WorkUnit_KicCloser() : protocols::mpi_refinement::WorkUnit_KicCloser
• WorkUnit_LoopHash() : protocols::loophash::WorkUnit_LoopHash , protocols::mpi_refinement::WorkUnit_LoopHash
• WorkUnit_MD() : protocols::mpi_refinement::WorkUnit_MD
• WorkUnit_MoverWrapper() : protocols::wum::WorkUnit_MoverWrapper
• WorkUnit_NormalMode() : protocols::mpi_refinement::WorkUnit_NormalMode
• WorkUnit_PartialAbinitio() : protocols::mpi_refinement::WorkUnit_PartialAbinitio
• WorkUnit_RamaPerturber() : protocols::mpi_refinement::WorkUnit_RamaPerturber
• WorkUnit_Relax() : protocols::mpi_refinement::WorkUnit_Relax
• WorkUnit_Sampler() : protocols::mpi_refinement::WorkUnit_Sampler
• WorkUnit_SilentStructStore() : protocols::wum::WorkUnit_SilentStructStore
• WorkUnit_Wait() : protocols::wum::WorkUnit_Wait
• WorkUnitBase() : protocols::wum::WorkUnitBase
• WorkUnitList() : protocols::wum::WorkUnitList
• WorkUnitManager : protocols::wum::WorkUnitBase , protocols::wum::WorkUnitManager
• WorkUnitQueue : protocols::wum::WorkUnitBase , protocols::wum::WorkUnitQueue
• WorkUnitQueue_Swapped : protocols::wum::WorkUnitManager , protocols::wum::WorkUnitQueue_Swapped
• worst_ : protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• worst_allowed_stub_bonus_ : protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover
• worst_combine_score_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• worst_top_energy_ : core::pack::annealer::MultiCoolAnnealer
• Wradius() : core::scoring::etable::Etable , core::scoring::etable::EtableOptions
• Wradius_ : core::scoring::etable::Etable
• wrap_dof_id() : protocols::environment::claims::EnvClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::XYZClaim
• wrapped_opt_min_ : protocols::optimize_weights::IterativeOptEDriver
• wrapped_phipsi_bins_ : protocols::match::VoxelSetIterator
• wrapped_phipsi_halfbins_ : protocols::match::VoxelSetIterator
• WrappedOptEExpressionCreator() : protocols::optimize_weights::WrappedOptEExpressionCreator
• WrapperOptEMultifunc() : protocols::optimize_weights::WrapperOptEMultifunc
• write() : core::chemical::ElectronConfiguration , core::chemical::Element , core::chemical::gasteiger::GasteigerAtomTypeData , core::grid::CartGrid< T > , core::io::serialization::BUFFER , protocols::abinitio::abscript::JumpSampleData , protocols::environment::AutoCutData , protocols::frag_picker::CSTalosIO , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::PhiPsiTalosIO , protocols::frag_picker::TorsionBinIO , protocols::matdes::ClashCheckFilter
• write2pdb() : protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::MutationsFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter
• write2pdb_ : protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::MutationsFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter
• write_ : protocols::matdes::ClashCheckFilter
• write_3Dprojection_kinemage() : protocols::match::OccupiedSpaceHash
• write_AA_kind_files_ : protocols::features::strand_assembly::SandwichFeatures
• write_ab_H3_kink_metrics_schema_to_db() : protocols::antibody::AntibodyFeatures
• write_ab_metrics_schema_to_db() : protocols::antibody::AntibodyFeatures
• write_all() : core::io::raw_data::RawFileData , core::io::silent::SilentFileData , protocols::hotspot_hashing::HotspotStubSet
• write_all_connect_info() : core::io::StructFileRepOptions
• write_all_connect_info_ : core::io::StructFileRepOptions
• write_all_info_files_ : protocols::features::strand_assembly::SandwichFeatures
• write_all_structs() : protocols::jd2::SilentFileJobOutputter
• write_apolar_hydrogens() : core::conformation::ResidueKinWriter
• write_apolar_hydrogens_ : core::conformation::ResidueKinWriter
• write_assignment() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Sparky , protocols::noesy_assign::PeakFileFormat_xpk
• write_assignment_indent() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Sparky , protocols::noesy_assign::PeakFileFormat_xpk
• write_assignment_stats() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Sparky , protocols::noesy_assign::PeakFileFormat_xpk
• write_assignments() : protocols::noesy_assign::NoesyModule , protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• write_atom_in_residue_pairs_table_schema() : protocols::features::AtomInResidueAtomInResiduePairFeatures
• write_atom_names() : protocols::noesy_assign::PeakFileFormat
• write_atom_names_ : protocols::noesy_assign::PeakFileFormat
• write_atom_pairs_table_schema() : protocols::features::AtomAtomPairFeatures
• write_atom_type_extra_parameters_table() : core::chemical::AtomTypeDatabaseIO
• write_atom_type_extra_parameters_table_schema() : core::chemical::AtomTypeDatabaseIO
• write_atom_type_properties_table() : core::chemical::AtomTypeDatabaseIO
• write_atom_type_properties_table_schema() : core::chemical::AtomTypeDatabaseIO
• write_atom_type_property_values_table_schema() : core::chemical::AtomTypeDatabaseIO
• write_atom_type_set_to_database() : core::chemical::AtomTypeDatabaseIO
• write_atom_type_table() : core::chemical::AtomTypeDatabaseIO
• write_atom_types_table_schema() : core::chemical::AtomTypeDatabaseIO
• write_atompot : core::scoring::APBSConfig::I_PARAM
• write_backbone_hydrogens() : core::conformation::ResidueKinWriter
• write_backbone_hydrogens_ : core::conformation::ResidueKinWriter
• write_beta_sheet_capping_info_ : protocols::features::strand_assembly::SandwichFeatures
• write_beta_turns_table_schema() : protocols::features::BetaTurnDetectionFeatures
• write_binary() : core::scoring::motif::XformScore
• write_binary_fa_dunbrack_libraries() : core::pack::dunbrack::RotamerLibrary
• write_binary_fa_dunbrack_libraries_02() : core::pack::dunbrack::RotamerLibrary
• write_binary_fa_dunbrack_libraries_10() : core::pack::dunbrack::RotamerLibrary
• write_bond_interres_angles_table_schema() : protocols::features::ProteinBondGeometryFeatures
• write_bond_interres_lengths_table_schema() : protocols::features::ProteinBondGeometryFeatures
• write_bond_intrares_angles_table_schema() : protocols::features::ProteinBondGeometryFeatures
• write_bond_intrares_lengths_table_schema() : protocols::features::ProteinBondGeometryFeatures
• write_bond_intrares_torsions_table_schema() : protocols::features::ProteinBondGeometryFeatures
• write_bundle_to_db() : protocols::features::helixAssembly::HelixBundleFeatures
• write_cache_to_db() : protocols::canonical_sampling::DbTrajectoryRecorder , protocols::trajectory::DbTrajectoryWriter
• write_cdr_metrics_schema_to_db() : protocols::antibody::AntibodyFeatures
• write_cdr_residue_schema_to_db() : protocols::antibody::AntibodyFeatures
• write_chain_B_resnum_ : protocols::features::strand_assembly::SandwichFeatures
• write_charge : core::scoring::APBSConfig::I_PARAM
• write_checkpoint() : protocols::canonical_sampling::MetropolisHastingsMover , protocols::forge::remodel::RemodelAccumulator , protocols::frag_picker::nonlocal::NonlocalFrags , protocols::genetic_algorithm::Entity , protocols::multistate_design::MultiStateEntity< T > , protocols::multistate_design::SingleStateEntityData
• write_circle_intersection_mask_to_kinemage() : core::pack::interaction_graph::InvRotamerDots
• write_clique_to_db() : protocols::features::ModelFeatures
• write_colors() : protocols::qsar::RenderGridsToKinemage
• write_comment() : core::io::silent::SilentFileData
• write_config() : core::scoring::PoissonBoltzmannPotential
• write_connollySurface_to_pdb() : protocols::pockets::ElectrostaticpotentialGrid
• write_constraints() : core::scoring::constraints::ConstraintIO
• write_coords() : core::conformation::ConformationKinWriter
• write_current_state_to_state_array() : protocols::flexpack::interaction_graph::FlexbbNode
• write_data() : core::fragment::FragmentIO , protocols::toolbox::match_enzdes_util::CstResInteractions , protocols::toolbox::match_enzdes_util::ResInteractions
• write_database() : protocols::backrub::BackrubProtocol , protocols::branch_angle::BranchAngleOptimizer
• write_db() : protocols::loophash::BackboneDB , protocols::loophash::LoopHashMap
• write_ddG_table_schema() : protocols::features::DdGFeatures
• write_decoys_to_hierarchy() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• write_diel : core::scoring::APBSConfig::I_PARAM
• write_downstream_coordinates() : protocols::match::output::DownstreamCoordinateKinemageWriter , protocols::match::output::SingleDownstreamResidueWriter
• write_dynamic_rsr_ : protocols::md::MDBase
• write_eggshell_to_pdb() : protocols::pockets::EggshellGrid
• write_eggshell_to_pdb_file() : protocols::pockets::NonPlaidFingerprint
• write_electrostatic_interactions_of_all_residues_ : protocols::features::strand_assembly::SandwichFeatures
• write_electrostatic_interactions_of_all_residues_in_a_strand_ : protocols::features::strand_assembly::SandwichFeatures
• write_electrostatic_interactions_of_surface_residues_in_a_strand_ : protocols::features::strand_assembly::SandwichFeatures
• write_empty_voxels_ : protocols::match::Bool3DGridKinemageWriter
• write_entities_checkpoint() : protocols::genetic_algorithm::GeneticAlgorithmBase
• write_espGrid_to_pdb() : protocols::pockets::ElectrostaticpotentialGrid
• write_exposed_dots_to_kinemage() : core::pack::interaction_graph::InvRotamerDots
• write_facets_ : protocols::match::Bool3DGridKinemageWriter
• write_file_ : protocols::match::output::MatchScoreWriter
• write_fold_tree_ : core::io::silent::RigidBodySilentStruct
• write_full_report() : protocols::features::ProteinSilentReport
• write_generations_checkpoint() : protocols::genetic_algorithm::GeneticAlgorithmBase
• write_geometric_solvation_table_schema() : protocols::features::GeometricSolvationFeatures
• write_grid_to_file() : protocols::match::Bool3DGridKinemageWriter
• write_grid_to_kinemage() : protocols::match::Bool3DGridKinemageWriter
• write_Grid_to_pdb() : protocols::pockets::EggshellGrid
• write_grids() : protocols::qsar::scoring_grid::GridManager
• write_HARO_orbital_table_schema() : protocols::features::OrbitalsFeatures
• write_hbond_chem_types_table_schema() : protocols::features::HBondFeatures
• write_hbond_dehydrons_table_schema() : protocols::features::HBondFeatures
• write_hbond_evaluation_types_table_schema() : core::scoring::hbonds::HBondDatabase
• write_hbond_fade_interval_table_schema() : core::scoring::hbonds::HBondDatabase
• write_hbond_geom_coords_table_schema() : protocols::features::HBondFeatures
• write_hbond_lennard_jones_table_schema() : protocols::features::HBondFeatures
• write_hbond_polynomial_1d_table_schema() : core::scoring::hbonds::HBondDatabase
• write_hbond_site_atoms_table_schema() : protocols::features::HBondFeatures
• write_hbond_site_environment_table_schema() : protocols::features::HBondFeatures
• write_hbond_sites_pdb_table_schema() : protocols::features::HBondFeatures
• write_hbond_sites_table_schema() : protocols::features::HBondFeatures
• write_hbonds_table_schema() : protocols::features::HBondFeatures
• write_header() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat_Sparky , protocols::noesy_assign::PeakFileFormat_xpk , protocols::qsar::RenderGridsToKinemage , protocols::rotamer_recovery::RRReporterHuman
• write_headers_to_hierarchy() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• write_heading_directions_of_all_AA_in_a_strand_ : protocols::features::strand_assembly::SandwichFeatures
• write_hist_to_file() : protocols::noesy_assign::FragsToAtomDist
• write_hist_to_stream() : protocols::noesy_assign::FragsToAtomDist
• write_HPOL_orbital_table_schema() : protocols::features::OrbitalsFeatures
• write_hydrogens() : core::conformation::ResidueKinWriter
• write_info_file() : protocols::jd2::archive::Batch
• write_int_area() : protocols::simple_filters::ShapeComplementarityFilter
• write_int_area_ : protocols::simple_filters::ShapeComplementarityFilter
• write_interface_residue_data_row_to_db() : protocols::features::InterfaceFeatures
• write_interface_residues_schema_to_db() : protocols::features::InterfaceFeatures
• write_interface_schema_to_db() : protocols::features::InterfaceFeatures
• write_interface_side_schema_to_db() : protocols::features::InterfaceFeatures
• write_kappa : core::scoring::APBSConfig::I_PARAM
• write_kin_header() : core::chemical::ResidueTypeKinWriter , core::conformation::ResidueKinWriter
• write_lines() : protocols::jd2::SingleFileBuffer , protocols::jd2::WriteFileSFB
• write_loop_AA_distribution_files_ : protocols::features::strand_assembly::SandwichFeatures
• write_loop_anchor_transforms_table_schema() : protocols::features::LoopAnchorFeatures
• write_loop_anchor_transforms_three_res_table_schema() : protocols::features::LoopAnchorFeatures
• write_loop_anchors_table_schema() : protocols::features::LoopAnchorFeatures
• write_loops_to_file() : protocols::loops::Loops
• write_loops_to_stream() : protocols::loops::Loops
• write_match_groups() : protocols::match::output::CloudPDBWriter
• write_match_scores() : protocols::match::output::MatchScoreWriter
• write_matchres_only_ : protocols::match::output::PDBWriter
• write_model() : protocols::canonical_sampling::DbTrajectoryRecorder , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::TrajectoryRecorder
• write_mse_summary() : protocols::simple_moves::DOFHistogramRecorder
• write_nchi_table_schema() : protocols::rotamer_recovery::RRReporterSQLite
• write_new_scorefile() : protocols::optimize_weights::IterativeOptEDriver
• write_nil_assignment() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Sparky , protocols::noesy_assign::PeakFileFormat_xpk
• write_only_highest_VC() : protocols::noesy_assign::PeakFileFormat_Base
• write_only_highest_VC_ : protocols::noesy_assign::PeakFileFormat_Base
• write_orbital_orbital_table_schema() : protocols::features::OrbitalsFeatures
• write_out_round_silent_file() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• write_out_silent_file() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• write_output_for_job() : protocols::jd3::JobOutputWriter
• write_output_from_job() : protocols::jd2::JobDistributor
• write_output_pose() : protocols::jd3::pose_outputters::PDBPoseOutputter , protocols::jd3::PoseOutputter
• write_p_aa_pp_files_ : protocols::features::strand_assembly::SandwichFeatures
• write_parameters_to_std_out() : protocols::optimize_weights::IterativeOptEDriver
• write_pdb_link_records() : core::io::StructFileRepOptions
• write_pdb_link_records_ : core::io::StructFileRepOptions
• write_pdb_parametric_info() : core::io::StructFileRepOptions
• write_pdb_parametric_info_ : core::io::StructFileRepOptions
• write_peak() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base , protocols::noesy_assign::PeakFileFormat_Sparky , protocols::noesy_assign::PeakFileFormat_xpk
• write_peak_files() : protocols::noesy_assign::CrossPeakList
• write_phi_psi_of_all_ : protocols::features::strand_assembly::SandwichFeatures
• write_phi_psi_of_E_ : protocols::features::strand_assembly::SandwichFeatures
• write_pocketGrid_to_pdb() : protocols::pockets::PocketGrid
• write_points() : protocols::qsar::RenderGridsToKinemage
• write_polar_hydrogens() : core::conformation::ResidueKinWriter
• write_polar_hydrogens_ : core::conformation::ResidueKinWriter
• write_pose() : core::io::raw_data::DecoyFileData , core::io::raw_data::ScoreFileData
• write_pot : core::scoring::APBSConfig::I_PARAM
• write_pqr() : core::scoring::PoissonBoltzmannPotential
• write_predicted_features_table_schema() : protocols::rotamer_recovery::RRReporterSQLite
• write_protein_backbone_atom_atom_pairs_table_schema() : protocols::features::ProteinBackboneAtomAtomPairFeatures
• write_protein_backbone_torsion_angles_table_schema() : protocols::features::ProteinBackboneTorsionAngleFeatures
• write_protein_rmsd_table_schema() : protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures
• write_protocol_report() : protocols::features::ProteinSilentReport
• write_psipred_ss2() : core::fragment::SecondaryStructure
• write_pymol_script() : protocols::flxbb::LayerDesignOperation
• write_pymol_string_to_pdb() : protocols::matdes::ClashCheckFilter , protocols::matdes::SymUnsatHbondFilter
• write_queue() : protocols::wum::WorkUnitManager
• write_queues_to_file() : protocols::wum::WorkUnitManager
• write_radius_of_gyration_table_schema() : protocols::features::RadiusOfGyrationFeatures
• write_rama_at_AA_to_files_ : protocols::features::strand_assembly::SandwichFeatures
• write_rama_score_all() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• write_report() : protocols::helical_bundle::PerturbBundle
• write_resfile() : protocols::simple_filters::SaveResfileToDiskFilter
• write_resfile_ : protocols::features::strand_assembly::SandwichFeatures
• write_resfile_NOT_FWY_on_surface_ : protocols::features::strand_assembly::SandwichFeatures
• write_resfile_to_minimize_too_many_core_heading_FWY_on_core_strands_ : protocols::features::strand_assembly::SandwichFeatures
• write_resfile_to_minimize_too_many_core_heading_FWY_on_edge_strands_ : protocols::features::strand_assembly::SandwichFeatures
• write_resfile_to_minimize_too_much_hydrophobic_surface_ : protocols::features::strand_assembly::SandwichFeatures
• write_resfile_when_seq_rec_is_bad_ : protocols::features::strand_assembly::SandwichFeatures
• write_residue_burial_table_schema() : protocols::features::ResidueBurialFeatures
• write_residue_pairs_table_schema() : protocols::features::PairFeatures
• write_residue_rotamers_table_schema() : protocols::features::RotamerFeatures
• write_residue_scores_1b_table_schema() : protocols::features::ResidueScoresFeatures
• write_residue_scores_2b_table_schema() : protocols::features::ResidueScoresFeatures
• write_residue_scores_2b_table_schema_helper() : protocols::features::ResidueScoresFeatures
• write_residue_scores_lr_2b_table_schema() : protocols::features::ResidueScoresFeatures
• write_residue_total_scores_table_schema() : protocols::features::ResidueTotalScoresFeatures
• write_residue_type_atom_table_schema() : core::chemical::ResidueDatabaseIO
• write_residue_type_bond_table_schema() : core::chemical::ResidueDatabaseIO
• write_residue_type_chi_rotamer_table_schema() : core::chemical::ResidueDatabaseIO
• write_residue_type_chi_table_schema() : core::chemical::ResidueDatabaseIO
• write_residue_type_cut_bond_table_schema() : core::chemical::ResidueDatabaseIO
• write_residue_type_icoor_table_schema() : core::chemical::ResidueDatabaseIO
• write_residue_type_property_table_schema() : core::chemical::ResidueDatabaseIO
• write_residue_type_proton_chi_table_schema() : core::chemical::ResidueDatabaseIO
• write_residue_type_table_schema() : core::chemical::ResidueDatabaseIO
• write_residue_type_variant_type_table_schema() : core::chemical::ResidueDatabaseIO
• write_residuetype_to_database() : core::chemical::ResidueDatabaseIO
• write_resonances() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• write_restype() : core::chemical::ResidueTypeKinWriter
• write_rotamer_boltzmann_weight_table_schema() : protocols::features::RotamerBoltzmannWeightFeatures
• write_rotamer_recovery_features_table_schema() : protocols::rotamer_recovery::RRReporterSQLite
• write_rotamer_recovery_full_table_schema() : protocols::rotamer_recovery::RRReporterSQLite
• write_rsd_coords() : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter
• write_salt_bridges_table_schema() : protocols::features::SaltBridgeFeatures
• write_schema_to_db() : core::chemical::AtomTypeDatabaseIO , core::chemical::ResidueDatabaseIO , protocols::antibody::AntibodyFeatures , protocols::antibody::clusters::CDRClusterFeatures , protocols::canonical_sampling::DbTrajectoryRecorder , protocols::features::AtomAtomPairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomTypesFeatures , protocols::features::BatchFeatures , protocols::features::BetaTurnDetectionFeatures , protocols::features::ChargeChargeFeatures , protocols::features::DdGFeatures , protocols::features::FeaturesReporter , protocols::features::GeometricSolvationFeatures , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::ConcurrencyTest , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::HelixCapFeatures , protocols::features::InterfaceFeatures , protocols::features::JobDataFeatures , protocols::features::LoopAnchorFeatures , protocols::features::ModelFeatures , protocols::features::OrbitalsFeatures , protocols::features::PairFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::ProteinBondGeometryFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ProteinSilentReport , protocols::features::ProtocolFeatures , protocols::features::RadiusOfGyrationFeatures , protocols::features::ResidueBurialFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::ResidueTypesFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::RuntimeFeatures , protocols::features::SaltBridgeFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TotalScoreFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures , protocols::rotamer_recovery::RRReporterSQLite , protocols::trajectory::DbTrajectoryWriter
• write_score_function_method_options_table_schema() : core::scoring::methods::EnergyMethodOptions
• write_score_function_weights_table_schema() : protocols::features::ScoreFunctionFeatures
• write_score_to_outfiles() : protocols::membrane::benchmark::SampleTiltAngles
• write_scorefile() : protocols::jd2::FileJobOutputter
• write_scorefile_ : protocols::jd2::FileJobOutputter
• write_separate_scorefile_ : protocols::jd2::SilentFileJobOutputter
• write_silent_struct() : core::conformation::symmetry::SymmetryInfo , core::io::silent::SilentFileData
• write_smol : core::scoring::APBSConfig::I_PARAM
• write_spanfile() : core::conformation::membrane::SpanningTopology
• write_strand_AA_distribution_files_ : protocols::features::strand_assembly::SandwichFeatures
• write_strength() : protocols::noesy_assign::PeakFileFormat , protocols::noesy_assign::PeakFileFormat_Base
• write_struct() : core::io::raw_data::DecoyFileData , core::io::raw_data::ScoreFileData
• write_stub() : protocols::hotspot_hashing::HotspotStubSet
• write_summary() : protocols::frag_picker::QuotaDebug
• write_talos_format() : protocols::noesy_assign::ResonanceList
• write_task_operation_residue_effects_table_schema() : protocols::features::TaskOperationFeatures
• write_task_operations_table_schema() : protocols::features::TaskOperationFeatures
• write_to_binary() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamerLibrary , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::rotamers::SingleResiduePeptoidLibrary
• write_to_binary_file() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData
• write_to_BRIX() : core::grid::CartGrid< T >
• write_to_compact_array() : core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::RotamerDotsCache
• write_to_disk() : protocols::sewing::Hasher
• write_to_file() : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N > , core::pack::rotamers::SingleBasicRotamerLibrary , core::pack::rotamers::SingleLigandRotamerLibrary , core::pack::rotamers::SingleResidueRotamerLibrary , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::contact_map::ContactMap , protocols::noesy_assign::FragsToAtomDist , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData
• write_to_file_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• write_to_pdb() : protocols::matdes::ClashCheckFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::MutationsFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::TaskAwareScoreTypeFilter
• write_to_stream() : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::contact_map::ContactMap , protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::FragsToAtomDist , protocols::noesy_assign::Resonance , protocols::noesy_assign::ResonanceList
• write_to_string() : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::canonical_sampling::BiasEnergy
• write_undefined_coef1() : protocols::branch_angle::BranchAngleOptimizer
• write_undefined_coef2() : protocols::branch_angle::BranchAngleOptimizer
• write_unrecognized_atoms_table_schema() : protocols::features::UnrecognizedAtomFeatures
• write_unrecognized_neighbors_table_schema() : protocols::features::UnrecognizedAtomFeatures
• write_unrecognized_residues_table_schema() : protocols::features::UnrecognizedAtomFeatures
• write_virtual_atoms() : core::conformation::ConformationKinWriter , core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• write_virtual_atoms_ : core::conformation::ConformationKinWriter , core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• write_water_hbond_geom_table_schema() : protocols::features::WaterFeatures
• write_work_unit() : protocols::wum::WorkUnitManager
• WRITEABLE_DATA : core::pose::datacache::CacheableDataType
• WriteableCacheableDataOP : protocols::abinitio::abscript::JumpSampleDataCreator , protocols::environment::AutoCutDataCreator
• WriteFileSFB() : protocols::jd2::WriteFileSFB
• WriteLigandMolFile() : protocols::ligand_docking::WriteLigandMolFile
• writeMRC() : core::scoring::electron_density::ElectronDensity
• WriteOut_MpiFileBuffer() : protocols::jd2::WriteOut_MpiFileBuffer
• writer_ : protocols::match::output::MatchProcessor
• WriteUpstreamCoordinateKinemage() : protocols::match::output::WriteUpstreamCoordinateKinemage
• WriteUpstreamHitKinemage() : protocols::match::output::WriteUpstreamHitKinemage
• wRMSD() : protocols::toolbox::DecoySetEvaluation
• WS_MethodIterator : core::scoring::ScoreFunction
• WS_Methods : core::scoring::ScoreFunction
• ws_methods_ : core::scoring::ScoreFunction
• ws_methods_begin() : core::scoring::ScoreFunction
• ws_methods_end() : core::scoring::ScoreFunction
• wsc_sc_ : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::weight_triple
• wt : core::scoring::dna::DirectReadoutPotential
• wt_ : protocols::canonical_sampling::PatchOperation , protocols::simple_moves::symmetry::SetupNCSMover
• wt_aa() : core::io::PositionDdGInfo::PositionDdGInfo
• wt_aa_ : core::io::PositionDdGInfo::PositionDdGInfo , protocols::optimize_weights::DDGMutationOptEData
• wt_adp_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc
• wt_ang_ : core::scoring::disulfides::FullatomDisulfidePotential
• wt_complexes_ : protocols::optimize_weights::DDGBindOptEData
• WT_COMPLEXES_LIST_FILE : protocols::optimize_weights::DDGBindOptEData
• wt_components_ : protocols::ddg::ddGMover
• wt_dens_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc
• wt_dihCS_ : core::scoring::disulfides::FullatomDisulfidePotential
• wt_dihSS_ : core::scoring::disulfides::FullatomDisulfidePotential
• wt_for_pro_in_1st_inter_sheet_loop_ : protocols::features::strand_assembly::SandwichFeatures
• wt_for_pro_in_3rd_inter_sheet_loop_ : protocols::features::strand_assembly::SandwichFeatures
• wt_for_pro_in_starting_loop_ : protocols::features::strand_assembly::SandwichFeatures
• wt_len_ : core::scoring::disulfides::FullatomDisulfidePotential
• wt_lk_ball_ : core::scoring::lkball::lkbtrie::LKBTrieEvaluator
• wt_lk_ball_iso_ : core::scoring::lkball::lkbtrie::LKBTrieEvaluator
• wt_lk_ball_wtd_ : core::scoring::lkball::lkbtrie::LKBTrieEvaluator
• wt_res_ : protocols::membrane::MPMutateRelaxMover
• wt_residue_ : protocols::pmut_scan::MutationData
• wt_residue_for_node() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• wt_score_components() : protocols::ddg::ddGMover
• wt_seqpos_for_node() : core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• wt_unbound_components_ : protocols::ddg::ddGMover
• wt_unbound_score_components() : protocols::ddg::ddGMover
• wt_unbounds_ : protocols::optimize_weights::DDGBindOptEData
• WT_UNBOUNDS_LIST_FILE : protocols::optimize_weights::DDGBindOptEData
• wt_unfolded_energies_emap_ : protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• wtD_ : protocols::simple_moves::symmetry::SetupNCSMover
• WTEBiasEnergy() : protocols::canonical_sampling::WTEBiasEnergy
• WtedClones : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo
• wts_ : protocols::optimize_weights::DDGMutationOptEData
• wu_desc_buf : protocols::boinc::BoincSharedMemory
• wu_desc_exists : protocols::boinc::BoincSharedMemory
• wu_type_ : protocols::wum::WorkUnitBase::WU_Header
• wum_ : protocols::wum::WorkUnitQueue_Swapped
• wus_ : protocols::wum::WorkUnitQueue