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

- d -

• d : protocols::simple_moves::MinimalRotamer
• d0 : protocols::hybridization::TMalign
• D0_MIN : protocols::hybridization::TMalign
• d0_out_ : protocols::hybridization::TMalign
• d0_search : protocols::hybridization::TMalign
• d0A : protocols::hybridization::TMalign
• d0B : protocols::hybridization::TMalign
• d12_ : protocols::toolbox::match_enzdes_util::LigandConformer
• d2 : protocols::normalmode::ContactStruct
• d23_ : protocols::toolbox::match_enzdes_util::LigandConformer
• d2target_ : core::scoring::constraints::ChainbreakDistFunc
• d77_48_lys_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_75g_mtsl_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_ctr_of_mass_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_end_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_trim_ctr_mass_ : protocols::ub_e2c::ubi_e2c_modeler
• d77_trim_end_ : protocols::ub_e2c::ubi_e2c_modeler
• d_ : protocols::scoring::methods::saxs::PDDFEnergy
• d_phi() : protocols::frag_picker::PhiPsiTalosIO
• d_psi() : protocols::frag_picker::PhiPsiTalosIO
• daemon_poses_ : protocols::pack_daemon::DaemonSet
• daemon_set() : protocols::pack_daemon::MultistateFitnessFunction
• daemon_set_ : protocols::pack_daemon::MultistateFitnessFunction
• daemon_tasks_ : protocols::pack_daemon::DaemonSet
• DaemonIndices : protocols::pack_daemon::DaemonSet
• DaemonList : protocols::pack_daemon::DaemonSet
• DaemonListIter : protocols::pack_daemon::DaemonSet
• daemons() : protocols::pack_daemon::DaemonSet
• daemons_ : protocols::pack_daemon::DaemonSet
• DaemonSet() : protocols::pack_daemon::DaemonSet
• dampen_ : protocols::normalmode::NormalModeMinimizer
• dangle_seq1_3prime_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• dangle_seq1_5prime_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• dangle_seq2_3prime_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• dangle_seq2_5prime_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• DarcParticleSwarmMinimizer() : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintBase , protocols::pockets::PlaidFingerprint
• DarcPSO_elsts_score_() : protocols::pockets::DarcParticleSwarmMinimizer
• DarcPSO_fp_compare_() : protocols::pockets::DarcParticleSwarmMinimizer
• data() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptEPositionData
• DATA : protocols::sparta::GDB
• data_ : protocols::analysis::InterfaceAnalyzerMover , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::frag_picker::JCouplingIO , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::scores::AdaptiveScoreHistogram , protocols::frag_picker::scores::AtomPairConstraintsScore , protocols::frag_picker::scores::DihedralConstraintsScore , protocols::frag_picker::scores::InterbondAngleScore , protocols::frag_picker::scores::JCoupling , protocols::loophash::BackboneDB , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::optimize_weights::OptEData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptEPositionData
• data_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• data_format_ : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• data_map_ : protocols::qsar::qsarOptFunc
• data_ndx_ : protocols::toolbox::KClusterElement
• database_filter_ : protocols::features::ProteinSilentReport
• database_fname() : protocols::toolbox::task_operations::DatabaseThread
• database_fname_ : protocols::toolbox::task_operations::DatabaseThread
• database_name_ : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter , protocols::rotamer_recovery::RRReporterSQLite
• database_pq_schema_ : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter , protocols::rotamer_recovery::RRReporterSQLite
• database_table() : protocols::toolbox::task_operations::ReadResfileFromDB
• database_table_ : protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::toolbox::task_operations::ReadResfileFromDB
• DatabaseEntryWorkUnit() : protocols::wum::DatabaseEntryWorkUnit
• DatabaseFilter() : protocols::features::DatabaseFilter
• DatabaseJobInputter() : protocols::features::DatabaseJobInputter
• DatabaseJobOutputter() : protocols::features::DatabaseJobOutputter
• DatabaseThread() : protocols::toolbox::task_operations::DatabaseThread
• DataBuffer() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• DataLoader() : protocols::jd2::parser::DataLoader
• dataloader_creator_map_ : protocols::jd2::parser::DataLoaderFactory
• DataLoaderCreator() : protocols::jd2::parser::DataLoaderCreator
• DataLoaderFactory() : protocols::jd2::parser::DataLoaderFactory
• DataLoaderRegistrator() : protocols::jd2::parser::DataLoaderRegistrator< T >
• DataMap : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::moves::DsspMover , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• DataPoint() : protocols::cluster::DataPoint
• dataset_ : protocols::toolbox::KClusterData
• datatype() : protocols::abinitio::abscript::JumpSampleData , protocols::environment::AutoCutData
• db_ : protocols::features::ProteinBondGeometryFeatures
• db_ang_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• DB_FNAME_LEVEL1_1 : protocols::sparta::ANN
• DB_FNAME_LEVEL1_2 : protocols::sparta::ANN
• DB_FNAME_LEVEL1_3 : protocols::sparta::ANN
• DB_FNAME_LEVEL2_1 : protocols::sparta::ANN
• DB_FNAME_LEVEL2_2 : protocols::sparta::ANN
• DB_FNAME_LEVEL2_3 : protocols::sparta::ANN
• db_len_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• DB_NAME_PREFIX : protocols::sparta::ANN
• DB_PATH : protocols::sparta::ANN
• db_path_ : protocols::antibody::AntibodyDatabaseManager , protocols::loophash::LoopHashLibrary
• db_session() : protocols::rotamer_recovery::RRReporterSQLite , protocols::toolbox::task_operations::ReadResfileFromDB
• db_session_ : protocols::antibody::AntibodyDatabaseManager , protocols::canonical_sampling::DbTrajectoryReader , protocols::features::ReportToDB , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::rotamer_recovery::RRReporterSQLite , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::trajectory::DbTrajectoryReader , protocols::wum::DatabaseEntryWorkUnit
• dbg_output_ : protocols::ddg::ddGMover
• DbTrajectoryReader() : protocols::canonical_sampling::DbTrajectoryReader , protocols::trajectory::DbTrajectoryReader
• DbTrajectoryRecorder() : protocols::canonical_sampling::DbTrajectoryRecorder
• DbTrajectoryWriter() : protocols::trajectory::DbTrajectoryWriter
• dcalibrate_ : protocols::noesy_assign::PeakAssignmentParameters , protocols::noesy_assign::StructureDependentPeakCalibrator
• dCOM_ : protocols::constraints_additional::COMCoordinateConstraint
• dcu0 : protocols::hybridization::TMalign
• dcut_ : protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::PeakAssignmentParameters
• ddG() : protocols::ddg::ddGMover
• ddg() : protocols::seeded_abinitio::GrowPeptides
• ddG() : protocols::simple_moves::ddG
• ddg_ : protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::seeded_abinitio::GrowPeptides
• ddg_based() : protocols::seeded_abinitio::SeedFoldTree
• ddg_based_ : protocols::seeded_abinitio::SeedFoldTree
• DDG_Bind_File_Index : protocols::optimize_weights::DDGBindOptEData
• ddG_bind_files_ : protocols::optimize_weights::IterativeOptEDriver
• ddG_bind_optE_data_ : protocols::optimize_weights::IterativeOptEDriver
• DDG_cutoff_ : protocols::pmut_scan::PointMutScanDriver
• ddG_cutoff_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• ddg_cycles_ : protocols::protein_interface_design::Revert
• ddG_filter_ : protocols::simple_filters::InterfaceBindingEnergyDensityFilter
• ddG_for_single_residue() : protocols::simple_filters::AlaScan , protocols::simple_filters::DdGScan
• ddG_mover() : protocols::simple_filters::DdGScan
• ddG_mover_ : protocols::simple_filters::DdGScan
• ddg_mut_wt_pairs_ : protocols::optimize_weights::IterativeOptEDriver
• ddG_mutation_data_ : protocols::optimize_weights::IterativeOptEDriver
• ddG_predictions_filename_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• ddG_scan_mover_ : protocols::features::DdGFeatures
• ddG_threshold() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::simple_filters::RotamerBoltzmannWeight
• ddG_threshold_ : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover
• ddg_threshold_ : protocols::simple_filters::DdgFilter
• ddG_threshold_ : protocols::simple_filters::RotamerBoltzmannWeight
• ddg_tolerance_ : protocols::protein_interface_design::Revert
• DDGBindOptEData() : protocols::optimize_weights::DDGBindOptEData
• ddGData() : protocols::ddG::ddGData
• DdGFeatures() : protocols::features::DdGFeatures
• DdGFeaturesCreator() : protocols::features::DdGFeaturesCreator
• DdgFilter() : protocols::simple_filters::DdgFilter
• ddGMover() : protocols::ddg::ddGMover
• DDGMutationOptEData() : protocols::optimize_weights::DDGMutationOptEData
• ddGs_ : protocols::optimize_weights::IterativeOptEDriver , protocols::simple_filters::RotamerBoltzmannWeight
• ddGs_binding_ : protocols::optimize_weights::IterativeOptEDriver
• DdGScan() : protocols::simple_filters::DdGScan
• dDist_dv1 : protocols::pockets::ray_distance_derivs
• dDist_dv2 : protocols::pockets::ray_distance_derivs
• dDist_dv3 : protocols::pockets::ray_distance_derivs
• dDist_dv4 : protocols::pockets::ray_distance_derivs
• dDist_dv5 : protocols::pockets::ray_distance_derivs
• dDist_dv6 : protocols::pockets::ray_distance_derivs
• ddomain_pot() : protocols::hybridization::DDomainParse
• DDomainParse() : protocols::hybridization::DDomainParse
• deallocate_arrays() : protocols::sparta::Sparta::SpartaLib
• deallocate_buffers() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::ParallelTempering
• debug() : protocols::antibody::SnugDock , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::checkpoint::CheckPointer , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::toolbox::task_operations::SeqprofConsensusOperation
• debug_ : protocols::anchored_design::AnchoredPerturbMover , protocols::anchored_design::AnchoredRefineMover , protocols::antibody::SnugDock , protocols::hybridization::CartesianSampler , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::simple_moves::MSDMover , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::task_operations::InteractingRotamerExplosion , protocols::toolbox::task_operations::SeqprofConsensusOperation
• debug_five() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_four() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_note_accepted_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_note_considered_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_note_projected_deltaE_of_considered_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_note_rejected_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_one() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_output() : protocols::ddg::ddGMover
• debug_print() : protocols::antibody::AntibodyNumberingParser
• debug_print_addresses() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• debug_print_hierarchy() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• debug_print_size_per_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• debug_three() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_two() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_zero() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debugging_output() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• DebugOut_MpiFileBuffer() : protocols::jd2::DebugOut_MpiFileBuffer
• decdisc_crystal_natives_ : protocols::optimize_weights::IterativeOptEDriver
• decdisc_decoy_poses_ : protocols::optimize_weights::IterativeOptEDriver
• decdisc_native_decoy_pairs_ : protocols::optimize_weights::IterativeOptEDriver
• decdisc_native_poses_ : protocols::optimize_weights::IterativeOptEDriver
• decdisc_xtal_natives_ : protocols::optimize_weights::IterativeOptEDriver
• decide_cuts() : protocols::hybridization::HybridizeFoldtreeDynamic
• decide_if_sequence_recovery_improved() : protocols::optimize_weights::IterativeOptEDriver
• decide_to_keep_pose() : protocols::stepwise::monte_carlo::mover::DeleteMover
• declare_all_rotamers_initialized() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• declare_chemical_bond() : protocols::environment::ProtectedConformation
• declare_energies_final() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• declare_minimization_over() : protocols::optimize_weights::OptEMultifunc
• declare_remodelable() : protocols::enzdes::EnzdesFlexibleRegion
• DeclareBond() : protocols::cyclic_peptide::DeclareBond
• decompose_structure() : protocols::medal::MedalMover , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate
• DecomposeAndReweightEnergiesCalculator() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• decoy_compatibility() : protocols::noesy_assign::PeakAssignment
• decoy_compatibility_ : protocols::noesy_assign::PeakAssignment
• decoy_count() : protocols::boinc::Boinc
• decoy_count_ : protocols::boinc::Boinc
• decoy_discrim_data_ : protocols::optimize_weights::IterativeOptEDriver
• decoy_iterator : protocols::jd2::archive::ArchiveBase
• decoy_loop_cutpoint_ : protocols::antibody_legacy::CDRH3Modeler
• decoys() : protocols::jd2::archive::ArchiveBase , protocols::wum::WorkUnit_SilentStructStore
• decoys_ : protocols::jd2::archive::ArchiveBase , protocols::optimize_weights::PNatStructureOptEData , protocols::wum::WorkUnit_SilentStructStore
• decoys_returned() : protocols::jd2::archive::Batch
• decoys_returned_to_archive_ : protocols::jd2::archive::Batch
• DecoySetEvaluation() : protocols::toolbox::DecoySetEvaluation
• decreasing() : protocols::loops::Loop , protocols::nonlocal::Region
• dEddofs_to_dEdvars() : protocols::normalmode::NormalModeMultifunc
• deep_optimization_ : protocols::antibody::GraftedStemOptimizer
• def_parameters : protocols::relax::CentroidRelax
• default_allow_bondangles() : protocols::helical_bundle::MakeBundle
• default_allow_bondangles_ : protocols::helical_bundle::MakeBundle
• default_allow_bondangles_set() : protocols::helical_bundle::MakeBundle
• default_allow_bondangles_set_ : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths() : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths_ : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths_set() : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths_set_ : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals() : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals_ : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals_set() : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals_set_ : protocols::helical_bundle::MakeBundle
• default_and_user_ : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• DEFAULT_APBS_PATH : protocols::pb_potential::SetupPoissonBoltzmannPotential
• default_bias_ : protocols::canonical_sampling::BiasEnergy
• default_build_hits_at_all_positions() : protocols::match::downstream::DownstreamAlgorithm
• default_crick_params_file() : protocols::helical_bundle::MakeBundle
• default_crick_params_file_ : protocols::helical_bundle::MakeBundle
• default_crick_params_file_set() : protocols::helical_bundle::MakeBundle
• default_crick_params_file_set_ : protocols::helical_bundle::MakeBundle
• default_delta_omega0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_omega0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_omega0_set() : protocols::helical_bundle::MakeBundle
• default_delta_omega0_set_ : protocols::helical_bundle::MakeBundle
• default_delta_omega1() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::PerturbBundle
• default_delta_omega1_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::PerturbBundle
• default_delta_omega1_all() : protocols::helical_bundle::MakeBundle
• default_delta_omega1_all_ : protocols::helical_bundle::MakeBundle
• default_delta_omega1_all_set() : protocols::helical_bundle::MakeBundle
• default_delta_omega1_all_set_ : protocols::helical_bundle::MakeBundle
• default_delta_t() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_t_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_t_set() : protocols::helical_bundle::MakeBundle
• default_delta_t_set_ : protocols::helical_bundle::MakeBundle
• default_displacement : protocols::hotspot_hashing::SICPatternAtTransform
• default_fold_tree_ : protocols::protein_interface_design::movers::PlaceStubMover
• default_helix_length() : protocols::helical_bundle::MakeBundle
• default_helix_length_ : protocols::helical_bundle::MakeBundle
• default_helix_length_set() : protocols::helical_bundle::MakeBundle
• default_helix_length_set_ : protocols::helical_bundle::MakeBundle
• default_instruction_path_ : protocols::antibody::design::AntibodySeqDesignMover
• default_invert() : protocols::helical_bundle::MakeBundle
• default_invert_ : protocols::helical_bundle::MakeBundle
• default_invert_set() : protocols::helical_bundle::MakeBundle
• default_invert_set_ : protocols::helical_bundle::MakeBundle
• default_master() : protocols::match::output::WriteUpstreamHitKinemage
• default_omega0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_omega0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_omega0_set() : protocols::helical_bundle::MakeBundle
• default_omega0_set_ : protocols::helical_bundle::MakeBundle
• default_omega1() : protocols::helical_bundle::MakeBundle
• default_omega1_ : protocols::helical_bundle::MakeBundle
• default_omega1_set() : protocols::helical_bundle::MakeBundle
• default_omega1_set_ : protocols::helical_bundle::MakeBundle
• default_options() : protocols::loophash::LoopHashLibraryLoader , protocols::loops::LoopsFileLoader , protocols::membrane::io::LipoFileLoader , protocols::membrane::io::SpanFileLoader , protocols::surface_docking::SurfaceVectorLoader
• default_precision_ : protocols::frag_picker::scores::FragmentScoreManager
• default_r0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_r0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_r0_set() : protocols::helical_bundle::MakeBundle
• default_r0_set_ : protocols::helical_bundle::MakeBundle
• default_repeats_ : protocols::relax::FastRelax
• default_residue_name() : protocols::helical_bundle::MakeBundle
• default_residue_name_ : protocols::helical_bundle::MakeBundle
• default_residue_name_set() : protocols::helical_bundle::MakeBundle
• default_residue_name_set_ : protocols::helical_bundle::MakeBundle
• default_sample_range_ : protocols::stepwise::monte_carlo::rna::RNA_TorsionMover
• DEFAULT_STATE : protocols::pb_potential::SetupPoissonBoltzmannPotential
• default_value() : protocols::helical_bundle::PerturbBundleOptions
• default_value_ : protocols::helical_bundle::PerturbBundleOptions
• default_width_ : protocols::frag_picker::scores::FragmentScoreManager
• default_z0_offset() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_z0_offset_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_z0_offset_set() : protocols::helical_bundle::MakeBundle
• default_z0_offset_set_ : protocols::helical_bundle::MakeBundle
• default_z1() : protocols::helical_bundle::MakeBundle
• default_z1_ : protocols::helical_bundle::MakeBundle
• default_z1_offset() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_z1_offset_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_z1_offset_set() : protocols::helical_bundle::MakeBundle
• default_z1_offset_set_ : protocols::helical_bundle::MakeBundle
• default_z1_set() : protocols::helical_bundle::MakeBundle
• default_z1_set_ : protocols::helical_bundle::MakeBundle
• define_active_site_from_gridlig_file() : protocols::match::MatcherTask
• define_active_site_from_residue_radii_list() : protocols::match::MatcherTask
• define_loops() : protocols::docking::DockingHighResLegacy
• define_match_by_single_downstream_positioning() : protocols::match::MatcherTask
• define_match_by_single_downstream_positioning_ : protocols::match::MatcherTask
• define_moving_res() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• define_start_window() : protocols::simple_moves::ClassicFragmentMover
• defined() : protocols::jumping::MembraneJump
• defined_positions() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• DefineMovableLoops() : protocols::seeded_abinitio::DefineMovableLoops
• defines_intrares_energy() : protocols::scoring::methods::InterchainPairEnergy
• definition_threshold_ : protocols::features::HBondFeatures
• definition_type_ : protocols::features::HBondFeatures
• defs2BuildPositions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• defs2BuildPositions_findts() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• degree() : protocols::sasa_scores::Poly
• degree_vicinity_ : protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• degrees : protocols::ligand_docking::Rotate_info
• degrees_ : protocols::ligand_docking::MinimizeLigand , protocols::nonlocal::HelixRotate
• delay_noesy_reassign_ : protocols::abinitio::IterativeBase
• delete_chain_ending() : protocols::environment::ProtectedConformation
• delete_checkpoints_ : protocols::checkpoint::CheckPointer
• delete_content_only() : protocols::simple_filters::FileRemoveFilter
• delete_content_only_ : protocols::simple_filters::FileRemoveFilter
• delete_db() : protocols::loophash::LoopHashLibrary
• delete_diagonal_peaks() : protocols::noesy_assign::CrossPeakList
• delete_in_progress_files() : protocols::jd2::FileSystemJobDistributor
• delete_interface_native_sidechains() : protocols::anchored_design::AnchoredDesignMover
• delete_interface_native_sidechains_ : protocols::anchored_design::AnchoredDesignMover
• delete_loop() : protocols::loops::Loops
• delete_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• delete_polymer_residue() : protocols::environment::ProtectedConformation
• delete_pose() : protocols::features::ProteinSilentReport
• delete_pose_from_tag() : protocols::features::ProteinSilentReport
• delete_record() : protocols::features::FeaturesReporter , protocols::features::JobDataFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::RotamerFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures
• delete_records_from_table() : protocols::features::FeaturesReporter
• delete_res_range_list_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• delete_residue() : protocols::frags::FragLib , protocols::frags::TorsionFragmentLibrary
• delete_residue_range_slow() : protocols::environment::ProtectedConformation
• delete_residue_slow() : protocols::environment::ProtectedConformation
• delete_virtual_residues_after_FastRelax_ : protocols::relax::FastRelax
• DeleteMover() : protocols::stepwise::monte_carlo::mover::DeleteMover
• DeleteRegionMover() : protocols::grafting::simple_movers::DeleteRegionMover
• delta() : protocols::dna::DNABase , protocols::helical_bundle::PerturbBundleOptions , protocols::moves::IteratedConvergenceMover , protocols::moves::TrialMover , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::LoopLengthChange , protocols::simple_moves::ContingentAcceptMover
• delta_ : protocols::dna::DNABase , protocols::moves::IteratedConvergenceMover , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::LoopLengthChange , protocols::scoring::methods::pcs2::GridSearchIterator , protocols::scoring::methods::pcs::GridSearchIterator , protocols::scoring::methods::pcsTs1::GridSearchIterator_Ts1 , protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 , protocols::scoring::methods::pcsTs3::GridSearchIterator_Ts3 , protocols::scoring::methods::pcsTs4::GridSearchIterator_Ts4 , protocols::simple_moves::ContingentAcceptMover
• delta_atr_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_atr_score_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_chi_zz() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• delta_coms : protocols::simple_filters::SymmetricMotifFilter
• delta_filter_thresholds() : protocols::protein_interface_design::filters::FilterScanFilter
• delta_filter_thresholds_ : protocols::protein_interface_design::filters::FilterScanFilter
• delta_filters() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::protein_interface_design::filters::FilterScanFilter
• delta_filters_ : protocols::protein_interface_design::filters::FilterScanFilter
• delta_grid_ : protocols::canonical_sampling::BiasEnergy::Histogram< T >
• delta_length_ : protocols::protein_interface_design::movers::PlaceOnLoop
• delta_omega0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_omega0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_omega1() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_omega1_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_omega1_all() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• delta_omega1_all_ : protocols::helical_bundle::parameters::BundleParameters
• delta_omega1_vals_output_ : protocols::helical_bundle::FitSimpleHelix
• delta_omega1_vect() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• delta_rep_score() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_rep_score_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_t() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_t_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_unsat_hbonds : protocols::analysis::InterfaceData
• delta_X_xx() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• delta_X_yy() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• delta_X_zz() : protocols::scoring::methods::pcs::PCS_tensor , protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1 , protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 , protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3 , protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• delta_z1() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• delta_z1_ : protocols::helical_bundle::parameters::BundleParameters
• delta_z1_vals_output_ : protocols::helical_bundle::FitSimpleHelix
• delta_z1_vect() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• deltaE_best() : protocols::enzdes::EnzdesFlexibleRegion
• DeltaFilter() : protocols::simple_filters::DeltaFilter
• deltaG_bind() : protocols::optimize_weights::DGBindOptEData
• deltaG_bind_ : protocols::optimize_weights::DGBindOptEData
• deltaT_ : protocols::canonical_sampling::BiasEnergy
• denovo_scorefxn_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol
• DenseIGRepacker() : protocols::pack_daemon::DenseIGRepacker
• DensePDInteractionGraphOP : protocols::pack_daemon::DenseIGRepacker
• density() : protocols::hybridization::FragmentBiasAssigner
• density_nbr() : protocols::hybridization::FragmentBiasAssigner
• density_redraw : protocols::viewer::GraphicsState
• density_sigma : protocols::viewer::GraphicsState
• DensityMorphingMover() : protocols::electron_density::DensityMorphingMover
• densityPtr : protocols::viewer::triangleIterator
• DensityScoringClaimer() : protocols::topology_broker::DensityScoringClaimer
• dependencies() : protocols::forge::build::BuildInstruction
• dependencies_ : protocols::forge::build::BuildInstruction
• dependencies_exist() : protocols::forge::build::BuildManager
• dependencies_satisfied() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• DependencyEdge : protocols::forge::build::BuildManager
• DependencyEdges : protocols::forge::build::BuildManager
• dependent_dof_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• dependent_on() : protocols::forge::build::BuildInstruction
• depth() : protocols::frag_picker::VallResidue
• depth_ : protocols::viewer::triangle
• deque_ : protocols::wum2::WUQueue
• deriv_check() : protocols::farna::RNA_Minimizer , protocols::simple_moves::MinMover
• deriv_check_ : protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc , protocols::farna::RNA_Minimizer , protocols::normalmode::NormalModeMultifunc
• deriv_check_local() : protocols::normalmode::NormalModeMinimizer
• deriv_check_result() : protocols::normalmode::NormalModeMinimizer
• deriv_check_result_ : protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeMultifunc
• deriv_check_verbose_ : protocols::normalmode::NormalModeMultifunc
• derive_from_src_lib() : protocols::frags::TorsionFragmentLibrary
• derive_peptide() : protocols::analysis::PeptideDeriverFilter
• derive_staple_constraints_() : protocols::simple_moves::PeptideStapleMover
• derived_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• derivs_of_ray_distances_ : protocols::pockets::PlaidFingerprint
• describe_fragments() : protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::PValuedFragmentScoreManager
• describe_score() : protocols::frag_picker::scores::BFactor , protocols::frag_picker::scores::DisulfideIdentity , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SequenceIdentity
• descriptors_ : protocols::features::ScreeningFeatures
• deserialize() : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeAtom , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::wum::DatabaseEntryWorkUnit , protocols::wum::WorkUnit_SilentStructStore , protocols::wum::WorkUnitBase
• design() : protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions , protocols::docking::DockingHighResLegacy
• DESIGN : protocols::flxbb::LayerDesignOperation
• design() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::simple_moves::DesignRepackMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol
• design_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions , protocols::docking::DockingHighResLegacy , protocols::docking::DockingProtocol , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::EnzRepackMinimize , protocols::seeded_abinitio::SeedSetupMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation
• design_all_aas() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_all_aas_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_antigen() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_antigen_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_chain1() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chain1_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chain2() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chain2_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chains_ : protocols::docking::DockTaskFactory
• design_foldpose_ : protocols::seeded_abinitio::SeedSetupMover
• design_framework() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_framework_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_framework_conservative_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_framework_conserved_res_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_info_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• design_layer() : protocols::flxbb::LayerDesignOperation
• design_layer_ : protocols::flxbb::LayerDesignOperation
• design_loop() : protocols::toolbox::task_operations::RestrictToLoops
• design_loops_ : protocols::toolbox::task_operations::RestrictToLoops
• design_matrix : protocols::forge::remodel::RemodelWorkingSet
• design_method_ : protocols::antibody::design::AntibodySeqDesignMover
• design_mode : protocols::forge::remodel::RemodelData
• design_mover() : protocols::simple_moves::MSDMover
• design_mover2_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• design_mover_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::simple_moves::MSDMover
• design_movers_ : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• design_neighbor : protocols::forge::remodel::RemodelData
• design_neighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• design_neighbors_ : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• design_only_target_residues() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• design_only_target_residues_ : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• design_partner1_ : protocols::simple_moves::DesignRepackMover
• design_partner2_ : protocols::simple_moves::DesignRepackMover
• design_peptide : protocols::flexpep_docking::FlexPepDockingFlags
• design_post_graft_ : protocols::antibody::design::AntibodyGraftDesignMover
• design_proline() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_proline_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_refine() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• design_refine_cart_relax() : protocols::forge::remodel::RemodelMover
• design_refine_seq_relax() : protocols::forge::remodel::RemodelMover
• design_res_ : protocols::seeded_abinitio::SeedSetupMover
• design_scorefxn_ : protocols::antibody::design::AntibodyDesignMover
• design_shell() : protocols::toolbox::task_operations::DesignAroundOperation
• design_shell_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::toolbox::task_operations::DesignAroundOperation
• design_strategy() : protocols::antibody::design::CDRSeqDesignOptions
• design_strategy_ : protocols::antibody::design::CDRSeqDesignOptions
• design_target_ : protocols::seeded_abinitio::SeedSetupMover
• design_target_res_ : protocols::enzdes::DetectProteinLigandInterface
• design_targets() : protocols::enzdes::EnzdesBaseProtocol
• design_targets_ : protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFlexibleRegion
• design_targets_score() : protocols::enzdes::EnzdesBaseProtocol
• design_taskset_ : protocols::flxbb::FlxbbDesign
• design_type : protocols::forge::remodel::LineObject
• designable : protocols::dna::PositionType
• DESIGNABLE : protocols::flxbb::LayerDesignOperation
• designable() : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::toolbox::task_operations::DatabaseThread
• designable_ : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::toolbox::task_operations::DatabaseThread
• designable_only() : protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter
• designable_only_ : protocols::outputter::ResFileOutputter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::symmetry::TaskAwareSymMinMover
• designable_residues_ : protocols::toolbox::match_enzdes_util::EnzdesSeqRecoveryCache
• designable_second_shell_ : protocols::dna::DesignProteinBackboneAroundDNA
• DesignableResiduesFilter() : protocols::protein_interface_design::filters::DesignableResiduesFilter
• DesignAroundOperation() : protocols::toolbox::task_operations::DesignAroundOperation
• designed_residue() : protocols::dna::PDBOutput
• designed_residues_ : protocols::dna::PDBOutput
• DesignInfo : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• DesignMinimizeHbonds() : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• DesignMoverFoldTreePair : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• DesignMoverRealPair : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover
• DesignProteinBackboneAroundDNA() : protocols::dna::DesignProteinBackboneAroundDNA
• DesignRepackMover() : protocols::simple_moves::DesignRepackMover
• DesignTask() : protocols::flxbb::DesignTask
• DesignTask_Layer() : protocols::flxbb::DesignTask_Layer
• DesignTask_Normal() : protocols::flxbb::DesignTask_Normal
• DesignTaskOP : protocols::flxbb::FlxbbDesign
• DesignTaskSet : protocols::flxbb::FlxbbDesign
• DesignVsNativeComparison() : protocols::enzdes::DesignVsNativeComparison
• desired_conformer_ : protocols::enzdes::ResidueConformerFilter
• desired_entity_history_size() : protocols::pack_daemon::TopEntitySet
• desired_entity_history_size_ : protocols::pack_daemon::TopEntitySet
• desired_loops() : protocols::LoopRebuild
• desired_remodel_ss_strings_ : protocols::enzdes::EnzdesFlexibleRegion
• desired_remodelres_in_vicinity() : protocols::forge::remodel::ResidueVicinityInfo
• desired_remodelres_in_vicinity_ : protocols::forge::remodel::ResidueVicinityInfo
• desired_sequence_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• desired_ss_chars_ : protocols::match::SecondaryStructureMPM
• desymmeterize() : protocols::match::upstream::DunbrackSCSampler
• desymmeterize_ : protocols::match::upstream::DunbrackSCSampler
• desymmeterize_upstream_restype_for_constraint() : protocols::match::Matcher
• detach() : protocols::moves::PyMolObserver
• detach_after_modify() : protocols::forge::build::BuildInstruction
• detach_after_modify_ : protocols::forge::build::BuildInstruction
• detach_from() : protocols::boinc::BoincCurrentPoseObserver , protocols::forge::build::BuildInstruction , protocols::viewer::ConformationViewer , protocols::viewer::SilentObserver
• detach_impl() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• detailed_balance() : protocols::canonical_sampling::CanonicalSamplingMover
• detailed_balance_ : protocols::canonical_sampling::CanonicalSamplingMover
• detailed_search() : protocols::hybridization::TMalign
• detect_and_set_camelid_CDR_H3_stem_type() : protocols::antibody::AntibodyInfo
• detect_and_set_regular_CDR_H3_stem_type() : protocols::antibody::AntibodyInfo
• detect_and_set_regular_CDR_H3_stem_type_new_rule() : protocols::antibody::AntibodyInfo
• detect_camelid_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• detect_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• detect_design_interface_ : protocols::enzdes::DetectProteinLigandInterface
• detect_disulfides() : protocols::environment::ProtectedConformation
• detect_regular_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• DetectProteinLigandInterface() : protocols::enzdes::DetectProteinLigandInterface
• DetectSymmetry() : protocols::simple_moves::symmetry::DetectSymmetry
• determine_all_match_relevant_downstream_atoms() : protocols::match::MatcherTask
• determine_atom_inds_for_restype() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• determine_best_constraint() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• determine_correct_length() : protocols::features::LoopAnchorFeatures
• determine_cyclization_viability() : protocols::simple_moves::DisulfideInsertionMover
• determine_dna_interface() : protocols::dna::DnaInterfaceFinder
• determine_flexible_regions() : protocols::enzdes::EnzdesFlexBBProtocol
• determine_found_residues_compatibility() : protocols::enzdes::SecondaryMatchProtocol
• determine_interface() : protocols::dna::DnaInterfaceFinder
• determine_job_ids_to_run() : protocols::jd2::MPIWorkPartitionJobDistributor
• determine_largest_nbr_atom_distance() : protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• determine_loop() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• determine_loops_to_model() : protocols::forge::remodel::RemodelLoopMover
• determine_protein_interface() : protocols::dna::DnaInterfaceFinder
• determine_ramachandran_hash() : protocols::features::BetaTurnDetection
• determine_ramachandran_hash_for_residue_with_dihedrals() : protocols::features::BetaTurnDetection
• determine_redundant_conformer_groups() : protocols::match::downstream::LigandConformerBuilder
• determine_redundant_upstream_matchres() : protocols::match::output::OutputWriter
• determine_res_cb_deviation() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• determine_res_to_recompute() : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• determine_score_variations() : protocols::jd2::archive::NormalizedEvaluatedArchive
• determine_target_downstream_res() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• determine_upstream_restypes() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• deviation() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• deviation_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• dfunc() : core::scoring::constraints::ChainbreakDistFunc , protocols::electron_density::BfactorMultifunc , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::normalmode::NormalModeMultifunc , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pockets::FingerprintMultifunc , protocols::pockets::PocketExemplarMultifunc , protocols::qsar::qsarOptFunc , protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd , protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1 , protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2 , protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3 , protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4
• dfunc_exact() : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• dfunc_numeric() : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• dG : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dG_binding_ : protocols::optimize_weights::IterativeOptEDriver
• dG_binding_data_ : protocols::optimize_weights::IterativeOptEDriver
• dG_bound_unbound_pairs_ : protocols::optimize_weights::IterativeOptEDriver
• dG_dSASA_ratio : protocols::analysis::InterfaceData
• DGBindOptEData() : protocols::optimize_weights::DGBindOptEData
• dhSASA : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dhSASA_rel_by_charge : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dhSASA_sc : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• diff_torsions : protocols::stepwise::modeler::rna::output_data_struct
• DiffAtomSasaFilter() : protocols::enzdes::DiffAtomSasaFilter
• difference_type : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• differentiate() : protocols::pack_daemon::ExpExpression , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::PowExpression , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VMax , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMin , protocols::pack_daemon::VMinBy
• diffuse_ring() : protocols::qsar::scoring_grid::SingleGrid
• dihedral_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• dihedral_rmsd() : protocols::frag_picker::DiversifyDihedralsSelector
• DihedralConstraintsScore() : protocols::frag_picker::scores::DihedralConstraintsScore
• dihedrallist : protocols::cartesian::MolecularDynamics
• dijkstras() : protocols::toolbox::ResidueNetwork
• dim() : protocols::pockets::PocketGrid , protocols::toolbox::ClusterBase
• dim_ : protocols::pockets::PocketGrid , protocols::toolbox::ClusterBase
• dim_prods_ : protocols::match::OccupiedSpaceHash
• dimension() : protocols::noesy_assign::CrossPeak
• dimer_seqsep_cutoff_ : protocols::fldsgn::potentials::sspot::SSPairPotential
• DimerPairing : protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::StrandPairingSet
• DimerPairings : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::StrandPairingSet
• dimprods_ : protocols::match::Bool3DGrid
• dimsizes() : protocols::match::Bool3DGrid
• dimsizes_ : protocols::match::Bool3DGrid
• DinucleotideStrand : protocols::farna::BasePairStep
• DinucleotideStrandSequence : protocols::farna::BasePairStepSequence
• dip_score_ : protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• dir() : protocols::jd2::archive::Batch
• dir_ : protocols::rigid::RigidBodyMover
• direction : protocols::hotspot_hashing::VectorPair
• direction_ : protocols::normalmode::NormalModeRelaxMover
• directory_ : protocols::ligand_docking::WriteLigandMolFile
• dis() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• dis_ : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• dis_D1D2_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• dis_D2D3_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• dis_U1D1() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• dis_U1D1_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• dis_U1D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• dis_U1D1_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• disAB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• disable() : protocols::ligand_docking::ResidueTorsionRestraints
• disable_autotemp() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• disable_build_stage() : protocols::loop_modeling::LoopModeler
• disable_centroid_stage() : protocols::loop_modeling::LoopModeler
• disable_constraint_scoreterms() : protocols::enzdes::EnzdesBaseProtocol
• disable_design_for_non_designing_cdrs() : protocols::antibody::design::AntibodySeqDesignTFCreator
• disable_fullatom_stage() : protocols::loop_modeling::LoopModeler
• disable_ignorefinished() : protocols::jobdist::BaseJobDistributor
• disable_inprogress() : protocols::jobdist::BaseJobDistributor
• disable_output() : protocols::jobdist::BaseJobDistributor
• disable_proline_design() : protocols::antibody::design::AntibodySeqDesignTFCreator
• disable_sampling_of_loop_takeoff() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• disable_sampling_of_loop_takeoff_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• disabled_ : protocols::checkpoint::CheckPointer , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• disallow_current_slide() : protocols::simple_moves::symmetry::SymmetrySlider
• disallow_deletion_of_last_residue_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• disallow_quench_ : protocols::toolbox::task_operations::ModifyAnnealer
• disallow_realign() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• disallow_realign_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• disallowed_host_pos_ : protocols::protein_interface_design::movers::PlaceStubMover
• disallowed_value_ : protocols::flxbb::FilterStructs_TotalCharge
• discard_jumps_ : protocols::topology_broker::FragmentJumpClaimer
• display_constraint_residues() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler
• display_func() : protocols::viewer::ConformationViewer
• display_if_necessary() : protocols::viewer::ConformationViewer
• display_progress() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• dist() : protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::frag_picker::Contact , protocols::frag_picker::PhiPsiTalosIO , protocols::hybridization::TMalign , protocols::pockets::UnionEdge , protocols::simple_filters::AlaScan , protocols::toolbox::ClusterBase
• dist2_cut() : protocols::normalmode::NormalMode
• dist2_cut_ : protocols::normalmode::NormalMode
• dist_ : protocols::fldsgn::SheetConstraintsRCG , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::forge::constraints::NtoC_RCG
• dist_bb() : protocols::protein_interface_design::filters::RmsdSimpleFilter
• dist_cutoff() : protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• dist_cutoff_ : protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• dist_list_ : protocols::toolbox::KClusterElement
• dist_sigma2_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• dist_square() : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::toolbox::KClusterData
• dist_squared() : protocols::frag_picker::Contact , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• dist_squared_ : protocols::frag_picker::Contact , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• dist_track() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• dist_track_ : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• dist_wts_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• distal_partition_res_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• distance : protocols::antibody::CDRPose , protocols::antibody::clusters::CDRCluster
• Distance : protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• distance() : protocols::hybridization::DDomainParse , protocols::noesy_assign::CovalentCompliance , protocols::noesy_assign::FragsToAtomDist , protocols::scoring::Interface , protocols::scoring::InterfaceInfo , protocols::toolbox::task_operations::RestrictToInterface
• distance_ : protocols::antibody::clusters::CDRCluster , protocols::contact_map::Contact , protocols::nonlocal::SheetTranslate , protocols::scoring::InterfaceInfo , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::symmetric_docking::SymRestrictTaskForDocking , protocols::toolbox::ClusterBase , protocols::toolbox::task_operations::RestrictToInterface
• distance_bin_width_ : protocols::qsar::scoring_grid::ShapeGrid
• distance_bound() : protocols::noesy_assign::CrossPeak
• distance_bound_ : protocols::noesy_assign::CrossPeak
• distance_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• distance_cutoff() : protocols::features::ChargeChargeFeatures , protocols::features::SaltBridgeFeatures , protocols::matdes::InterfacePackingFilter
• distance_cutoff_ : protocols::contact_map::ContactMap , protocols::features::ChargeChargeFeatures , protocols::features::SaltBridgeFeatures , protocols::matdes::InterfacePackingFilter , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::seeded_abinitio::CAcstGenerator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::PiPiCalculator , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator
• distance_cutoff_for_electrostatic_interactions_ : protocols::features::strand_assembly::SandwichFeatures
• distance_matrix : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• distance_matrix_ : protocols::contact_map::ContactMap
• distance_pair() : protocols::simple_moves::symmetry::SetupNCSMover
• distance_pair_ : protocols::simple_moves::symmetry::SetupNCSMover
• distance_record() : protocols::noesy_assign::FragsToAtomDist
• distance_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• distance_squared() : protocols::frag_picker::VallResidue
• distance_squared_ : protocols::scoring::Interface
• distance_squared_cb() : protocols::frag_picker::VallResidue
• distance_squared_cen() : protocols::frag_picker::VallResidue
• distance_threshold() : protocols::matdes::OligomericAverageDegreeFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::ResidueBurialFilter
• distance_threshold_ : protocols::enzdes::LigBurialFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::simple_filters::AlaScan , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::toolbox::task_operations::ProteinCore
• distance_weights_ : protocols::frag_picker::scores::ProfileScoreDistWeight
• DistanceBoundVector : protocols::noesy_assign::DistanceScoreMover
• distanceFromStart : protocols::toolbox::Node
• DistanceRecord() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• DistanceScoreMover() : protocols::noesy_assign::DistanceScoreMover
• DistanceSquared : protocols::flexpack::interaction_graph::OTFFlexbbNode
• disth : protocols::kinmatch::KRSQuery
• distinguish_pucker() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• distinguish_pucker_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• distribute_jobs_to_remote_daemons() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• distribute_over_mpi_ : protocols::optimize_weights::OptEMultifunc
• distribution : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Translate_info
• distribution_map_ : protocols::ligand_docking::DistributionMap
• DistributionMap() : protocols::ligand_docking::DistributionMap
• distThresh_ : protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter
• disulf_fa_max_ : protocols::forge::remodel::RemodelMover
• disulf_file_ : protocols::hybridization::HybridizeProtocol
• disulfide_cutpoint : protocols::forge::remodel::RemodelWorkingSet
• disulfide_data_ : protocols::frag_picker::scores::DisulfideDistance
• disulfide_file_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• disulfide_jump_points : protocols::forge::remodel::RemodelWorkingSet
• disulfide_list() : protocols::protein_interface_design::movers::DisulfideMover
• disulfide_ss : protocols::forge::remodel::RemodelWorkingSet
• DisulfideDistance() : protocols::frag_picker::scores::DisulfideDistance
• DisulfideEntropyFilter() : protocols::simple_filters::DisulfideEntropyFilter
• DisulfideFilter() : protocols::protein_interface_design::filters::DisulfideFilter
• DisulfideIdentity() : protocols::frag_picker::scores::DisulfideIdentity
• DisulfideInsertionMover() : protocols::simple_moves::DisulfideInsertionMover
• DisulfideInsertionMoverCreator() : protocols::simple_moves::DisulfideInsertionMoverCreator
• DisulfideList : protocols::denovo_design::DisulfidizeMover
• DisulfideMover() : protocols::protein_interface_design::movers::DisulfideMover
• disulfides() : protocols::simple_moves::ForceDisulfidesMover
• disulfides_ : protocols::simple_moves::ForceDisulfidesMover
• DisulfidizeMover() : protocols::denovo_design::DisulfidizeMover
• DisulfJumpClaimer() : protocols::topology_broker::DisulfJumpClaimer
• disulfLandingRange : protocols::forge::remodel::RemodelData
• disulfMobileRange : protocols::forge::remodel::RemodelData
• DisulfPairing() : protocols::jumping::DisulfPairing
• DisulfPairingLibrary() : protocols::jumping::DisulfPairingLibrary
• disulfs_ : protocols::hybridization::MRMover
• DisulfTemplate() : protocols::jumping::DisulfTemplate
• DisulfTemplateList : protocols::jumping::DisulfPairingLibrary
• DisulfTemplateMap : protocols::jumping::DisulfPairingLibrary
• diversify() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• diversify_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• diversify_all_confs() : protocols::enzdes::DiversifyStoredRBConfs
• diversify_backbone_only_rotamers() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• diversify_cst_conformers() : protocols::jumping::ResiduePairJump
• diversify_dof_conformers() : protocols::jumping::ResiduePairJump
• diversify_loop_only_ : protocols::loophash::LoopHashDiversifier
• DiversifyCrmsdByClustering() : protocols::frag_picker::DiversifyCrmsdByClustering
• DiversifyCrmsdSelector() : protocols::frag_picker::DiversifyCrmsdSelector
• DiversifyDihedralsSelector() : protocols::frag_picker::DiversifyDihedralsSelector
• DiversifyStoredRBConfs() : protocols::enzdes::DiversifyStoredRBConfs
• divide_up_mutations() : protocols::pmut_scan::PointMutScanDriver
• divide_up_pdbs() : protocols::optimize_weights::IterativeOptEDriver
• dle_flag_ : protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• dlig_nmeg_limit_ : protocols::pack_daemon::DaemonSet
• dmatrix_ : protocols::scoring::methods::saxs::PDDFEnergy
• DME_FilterMover() : protocols::simple_moves::DME_FilterMover
• dme_threshold_ : protocols::simple_moves::DME_FilterMover
• dmp_pdb_ : protocols::ddg::ddGMover
• dna_base_positions_ : protocols::dna::DNAParameters
• dna_chains() : protocols::dna::RestrictDesignToProteinDNAInterface
• dna_chains_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface
• dna_design_ : protocols::motifs::MotifDnaPacker
• dna_move_ : protocols::relax::FastRelax
• dna_neighbors() : protocols::dna::DnaInterfaceFinder
• dna_neighbors_ : protocols::dna::DnaInterfaceFinder
• dna_packer_ : protocols::motifs::MotifDnaPacker
• dna_positions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dna_positions_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dna_seq_tag() : protocols::dna::DnaInterfacePacker
• dna_sequences_ : protocols::dna::DnaInterfacePacker
• DNABase() : protocols::dna::DNABase
• DNABasepair() : protocols::dna::DNABasepair
• DNABasestep() : protocols::dna::DNABasestep
• DnaChains() : protocols::dna::DnaChains
• DnaDesignDef() : protocols::dna::DnaDesignDef
• DnaDesignDefOP : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• DnaDesignDefOPs : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• DnaInterfaceFinder() : protocols::dna::DnaInterfaceFinder
• DnaInterfaceMinMover() : protocols::dna::DnaInterfaceMinMover
• DnaInterfaceMultiStateDesign() : protocols::dna::DnaInterfaceMultiStateDesign
• DnaInterfacePacker() : protocols::dna::DnaInterfacePacker
• DnaNeighbor() : protocols::dna::DnaNeighbor
• DNAParameters() : protocols::dna::DNAParameters
• DnaPosition() : protocols::dna::DnaPosition
• do_add_delete_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• do_align_ : protocols::protein_interface_design::filters::RmsdSimpleFilter
• do_append() : protocols::stepwise::monte_carlo::mover::AddMover
• do_apply() : protocols::kinematic_closure::KicMover , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopModeler , protocols::loop_modeling::LoopMover , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::samplers::LegacyKicSampler , protocols::loop_modeling::utilities::AcceptanceCheck , protocols::loop_modeling::utilities::LoopFilter , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::loop_modeling::utilities::PrepareForCentroid , protocols::loop_modeling::utilities::PrepareForFullatom
• do_caching() : protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::AtomBasedConstraintsScore , protocols::frag_picker::scores::CachingScoringMethod , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::GunnCostScore , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::JCoupling , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::RDCScore , protocols::frag_picker::scores::ScoreEValuator , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity
• do_caching_simple() : protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• do_calibration() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::PeakCalibratorMap
• do_chain_closure_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• do_chain_closure_modeler() : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• do_checks() : protocols::stepwise::modeler::align::StepWisePoseAligner
• do_checks_ : protocols::stepwise::modeler::align::StepWiseClusterer
• do_checks_and_apply_protonated_H1_adenosine_variant() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• do_close_loops_ : protocols::farna::RNA_DeNovoProtocol
• do_clustering() : protocols::cluster::ClusterPhilStyle , protocols::stepwise::modeler::StepWiseMinimizer , protocols::toolbox::ClusterPhilStyle
• do_compute_jump_rmsd() : protocols::nonlocal::StarTreeBuilder
• do_cter_insert_ : protocols::antibody::ModelCDRH3
• do_distributed_rerun() : protocols::abinitio::AbrelaxApplication
• do_dump_pdb_ : protocols::farna::RNA_Minimizer
• do_dynamic_patching() : protocols::abinitio::IterativeBase
• do_final_repack() : protocols::relax::CentroidRelax
• do_frag_cycles() : protocols::loops::loop_closure::ccd::LoopClosure
• do_full_minimizing() : protocols::stepwise::modeler::StepWiseMinimizer
• do_h3_modeling_ : protocols::antibody_legacy::CDRH3Modeler
• do_hardsphere_bump_check_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• do_init() : protocols::rpc::BasicCmdLineInit , protocols::rpc::BasicInit
• do_initialize() : protocols::md::CartesianMD
• do_intrastage_docking() : protocols::hybridization::HybridizeProtocol
• do_loop_closure() : protocols::medal::MedalMover
• do_main_loop() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• do_matching() : protocols::enzdes::SecondaryMatchProtocol
• do_MD() : protocols::md::CartesianMD
• do_md() : protocols::relax::FastRelax
• do_minimize() : protocols::md::CartesianMD , protocols::relax::FastRelax , protocols::stepwise::modeler::StepWiseMinimizer
• do_minimize_ : protocols::simple_moves::CombinePoseMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• do_minimizing() : protocols::stepwise::modeler::StepWiseModeler
• do_not_connect_sheets_by_loops_ : protocols::features::strand_assembly::SandwichFeatures
• do_not_sample_multiple_virtual_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• do_not_sample_multiple_virtual_sugar_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• do_not_write_resfile_of_sandwich_that_has_non_canonical_LR_ : protocols::features::strand_assembly::SandwichFeatures
• do_packing() : protocols::stepwise::modeler::packer::StepWisePacker
• do_prepack() : protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• do_prepacking() : protocols::stepwise::modeler::StepWiseModeler
• do_prepend() : protocols::stepwise::monte_carlo::mover::AddMover
• do_rama_check_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• do_random_fragment_insertions() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• do_random_moves() : protocols::farna::RNA_DeNovoProtocol
• do_redistribution() : protocols::cluster::ClusterPhilStyle
• do_rerun() : protocols::abinitio::AbrelaxApplication
• do_rotation() : protocols::hybridization::TMalign
• do_same_strand() : protocols::jumping::SameStrand
• do_sampling() : protocols::stepwise::modeler::StepWiseModeler
• do_sanity_check_ : protocols::loophash::LoopHashLibrary
• do_score() : protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::PNatLigPoseOptEData
• do_screen() : protocols::stepwise::screener::AlignRMSD_Screener
• do_screen_ : protocols::stepwise::screener::AlignRMSD_Screener
• do_screening_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• do_screens_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• do_sfxn_eval_every_iteration_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• do_some_clustering() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• do_some_filtering() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• do_stage1_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage2_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage3_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage3b_cycles() : protocols::abinitio::MembraneAbinitio
• do_stage4_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage5_cycles() : protocols::abinitio::ClassicAbinitio
• do_step() : protocols::abinitio::abscript::AbscriptMover::StageTracker
• do_strand_sum() : protocols::jumping::SameStrand
• do_sugar_sampling() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• do_superimposition() : protocols::stepwise::modeler::align::StepWisePoseAligner
• do_test_move() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• do_the_modeler() : protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator
• do_the_move() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• doAngleDerivatives() : protocols::cartesian::MolecularDynamics
• doBondDerivatives() : protocols::cartesian::MolecularDynamics
• dock_chains_ : protocols::analysis::InterfaceAnalyzerMover
• dock_design_filter_map_ : protocols::protein_interface_design::DockDesignFilterFactory
• dock_design_loop_num_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• dock_high_res() : protocols::antibody::design::AntibodyDesignModeler
• dock_into_dens_strategy_ : protocols::electron_density::SetupForDensityScoringMover
• dock_low_res() : protocols::antibody::design::AntibodyDesignModeler
• dock_lowres_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dock_lowres_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dock_mcm_ : protocols::docking::DockMCMProtocol , protocols::surface_docking::FullatomRelaxMover
• dock_mcm_cycle_ : protocols::docking::DockMCMCycle
• dock_mcm_on_surface() : protocols::surface_docking::FullatomRelaxMover
• dock_mcm_protocol_ : protocols::antibody::RefineBetaBarrel
• dock_min_ : protocols::docking::DockingProtocol
• dock_pert_ : protocols::docking::DockingInitialPerturbation
• dock_post_graft_ : protocols::antibody::design::AntibodyGraftDesignMover
• dock_ppk_ : protocols::docking::DockingPrepackProtocol , protocols::symmetric_docking::SymDockProtocol
• dock_rounds_ : protocols::antibody::design::AntibodyGraftDesignMover
• dock_scorefxn_ : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel
• dock_scorefxn_highres_ : protocols::antibody::AntibodyModelerProtocol
• dock_trials_ : protocols::enzdes::PredesignPerturbMover
• DockAndRetrieveSidechains() : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• DockDesignFilterFactory() : protocols::protein_interface_design::DockDesignFilterFactory
• dockfa_cst_min_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dockfa_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dockfa_min_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• dockfa_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• docking() : protocols::antibody::SnugDockProtocol
• docking_ : protocols::antibody::SnugDockProtocol
• docking_constraint_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_frequency() : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• docking_frequency_ : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• docking_ft_ : protocols::protein_interface_design::movers::SetAtomTree
• docking_high_ : protocols::symmetric_docking::SymDockProtocol
• docking_highres_filter() : protocols::symmetric_docking::SymDockProtocol
• docking_highres_mover() : protocols::docking::DockingProtocol
• docking_highres_mover_ : protocols::docking::DockingProtocol
• docking_highres_protocol_mover_ : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• docking_jump() : protocols::topology_broker::AsymFoldandDockClaimer
• docking_jump_ : protocols::topology_broker::AsymFoldandDockClaimer
• docking_local_refine_ : protocols::antibody_legacy::CDRH3Modeler , protocols::docking::DockingProtocol , protocols::topology_broker::AsymFoldandDockClaimer
• docking_low_ : protocols::symmetric_docking::SymDockProtocol
• docking_lowres_filter() : protocols::symmetric_docking::SymDockProtocol
• docking_lowres_mover() : protocols::docking::DockingProtocol
• docking_lowres_mover_ : protocols::docking::DockingProtocol
• docking_lowres_protocol_ : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• docking_map_ : protocols::ub_e2c::ubi_e2c_modeler
• docking_mover_ : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• docking_protocol_ : protocols::docking::membrane::MPDockingMover
• docking_score_high_ : protocols::symmetric_docking::SymDockProtocol
• docking_score_high_min_ : protocols::symmetric_docking::SymDockProtocol
• docking_score_low_ : protocols::symmetric_docking::SymDockProtocol
• docking_score_pack_ : protocols::symmetric_docking::SymDockProtocol
• docking_scorefxn_high_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_scorefxn_low_ : protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_scorefxn_output_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_scorefxn_pack_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• DockingEnsemble() : protocols::docking::DockingEnsemble
• DockingEnsemblePrepackProtocol() : protocols::docking::DockingEnsemblePrepackProtocol
• DockingHighRes() : protocols::docking::DockingHighRes
• DockingHighResFilter() : protocols::docking::DockingHighResFilter
• DockingHighResLegacy() : protocols::docking::DockingHighResLegacy
• DockingInitialPerturbation() : protocols::docking::DockingInitialPerturbation
• DockingLowRes() : protocols::docking::DockingLowRes
• DockingLowResEnsemble() : protocols::docking::DockingLowResEnsemble
• DockingLowResFilter() : protocols::docking::DockingLowResFilter
• DockingNoRepack1() : protocols::toolbox::task_operations::DockingNoRepack1
• DockingNoRepack2() : protocols::toolbox::task_operations::DockingNoRepack2
• DockingPrepackProtocol() : protocols::docking::DockingPrepackProtocol
• DockingProtocol() : protocols::docking::DockingProtocol
• DockingSlideIntoContact() : protocols::docking::DockingSlideIntoContact
• DockMCMCycle() : protocols::docking::DockMCMCycle
• DockMCMProtocol() : protocols::docking::DockMCMProtocol
• DockMinMover() : protocols::docking::DockMinMover
• DockSetupMover() : protocols::docking::DockSetupMover
• DockTaskFactory() : protocols::docking::DockTaskFactory
• DockWithHotspotMover() : protocols::protein_interface_design::movers::DockWithHotspotMover
• doDihedralDerivatives() : protocols::cartesian::MolecularDynamics
• does_final_fold_tree_exist() : protocols::topology_broker::TopologyBroker
• DOES_NOT_CONTROL : protocols::environment::claims::ClaimStrength
• dof() : protocols::rigid::RigidBodyDofPerturbMover , protocols::sic_dock::CorrectionVisitor
• dof_ : protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofRandomizeMover , protocols::rigid::RigidBodyDofTransMover
• dof_conformers_ : protocols::jumping::ResiduePairJump
• DoF_helix_index() : protocols::helical_bundle::BundleGridSamplerHelper
• dof_id_ranges() : protocols::backrub::BackrubMover , protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SmallMover
• dof_ids1_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• dof_ids2_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• dof_ids_ : protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• dof_lower_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• DoF_name() : protocols::helical_bundle::BundleGridSamplerHelper
• dof_sample_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• DoF_sample_value() : protocols::helical_bundle::BundleGridSamplerHelper
• dof_samples_ : protocols::helical_bundle::BundleGridSamplerHelper
• DOF_TaskMap : protocols::simple_moves::MinMover
• dof_tasks_ : protocols::simple_moves::MinMover
• DoF_type() : protocols::helical_bundle::BundleGridSamplerHelper
• dof_upper_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• dof_values_ : protocols::simple_moves::DOFHistogramRecorder
• dof_variables_ : protocols::optimize_weights::WrapperOptEMultifunc
• DofClaim() : protocols::topology_broker::claims::DofClaim
• DOFElement() : protocols::environment::claims::DOFElement
• DOFElemVect : protocols::environment::EnvClaimBroker
• DOFHistogramRecorder() : protocols::simple_moves::DOFHistogramRecorder
• dofmover_compresses() : protocols::simple_moves::symmetry::SymmetrySlider
• DofPassportCOP : protocols::environment::ClientMover
• dofs() : protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::simple_moves::DOFHistogramRecorder
• dofs_ : protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyDofSeqRandomizeMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::simple_moves::DOFHistogramRecorder , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::simple_moves::symmetry::SymDockingSlideIntoContact , protocols::simple_moves::symmetry::SymmetrySlider
• dofs_for_pose0() : protocols::normalmode::NormalModeMultifunc
• dofs_for_pose0_ : protocols::normalmode::NormalModeMultifunc
• dofs_to_vars() : protocols::normalmode::NormalModeMultifunc
• DofUnlock() : protocols::environment::DofUnlock , protocols::environment::ProtectedConformation
• doKIC() : protocols::generalized_kinematic_closure::GeneralizedKIC
• domain_map : protocols::cartesian::MolecularDynamics
• domain_move_frequency_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• domain_parse_templates() : protocols::hybridization::HybridizeProtocol
• DomainAssembly() : protocols::abinitio::DomainAssembly , protocols::hybridization::DomainAssembly
• DomainInterfaceFilter() : protocols::simple_filters::DomainInterfaceFilter
• domains_all_templ_ : protocols::hybridization::HybridizeProtocol
• doMD() : protocols::cartesian::MolecularDynamics
• dominant() : protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• dominant_ : protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• doMinimising() : protocols::cartesian::MolecularDynamics
• don_dist_cutoff() : protocols::features::WaterFeatures
• don_dist_cutoff_ : protocols::features::WaterFeatures
• donor_atom_xyz_list_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• donor_base_atom_xyz_list_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• donorList : protocols::sparta::PDB
• donors : protocols::sic_dock::EdgeStandScore
• donors_ : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• dont_be_lenient() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• dont_check_overlap() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• dont_check_rama() : protocols::kinematic_closure::solution_pickers::FilteredSolutions
• dotscore_ : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• double_lazy_ : protocols::toolbox::task_operations::SetIGTypeOperation
• double_mutant_scan_ : protocols::pmut_scan::PointMutScanDriver
• DoubleDenseIGRepacker() : protocols::pack_daemon::DoubleDenseIGRepacker
• DoubleDensePDInteractionGraphOP : protocols::pack_daemon::DoubleDenseIGRepacker
• DoubleLayerKinematicAbinitio() : protocols::abinitio::DoubleLayerKinematicAbinitio
• down_jump_atom_ : protocols::simple_filters::JumpEvaluator
• down_stub_ : protocols::simple_filters::JumpEvaluator
• downhill_accepts_ : protocols::moves::MoverStatistics
• downstream_algorithms() : protocols::match::Matcher
• downstream_algorithms_ : protocols::match::Matcher
• downstream_atom_coordinates_needed_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• downstream_atom_inds_used_in_matching_ : protocols::match::MatcherTask
• downstream_atoms_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• downstream_atoms_required_inside_active_site() : protocols::match::MatcherTask
• downstream_atoms_required_inside_active_site_ : protocols::match::Matcher , protocols::match::MatcherTask
• downstream_builder() : protocols::match::Matcher
• downstream_builders() : protocols::match::Matcher
• downstream_builders_ : protocols::match::Matcher
• downstream_chains_ : protocols::analysis::InterfaceAnalyzerMover
• downstream_conf_id() : protocols::match::downstream_hit , protocols::match::Hit , protocols::match::match_dspos1
• downstream_conf_id_ : protocols::match::downstream_hit
• downstream_hit() : protocols::match::downstream_hit
• downstream_orientation_atoms() : protocols::match::MatcherTask
• downstream_orientation_atoms_ : protocols::match::Matcher , protocols::match::MatcherTask
• downstream_pose() : protocols::match::Matcher , protocols::match::MatcherTask
• downstream_pose_ : protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::output::UpstreamDownstreamCollisionFilter
• downstream_pose_from_hit() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• downstream_pose_from_task_ : protocols::match::output::PDBWriter
• downstream_res() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• downstream_res_nr() : protocols::jumping::JumpSample
• downstream_restype_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• DownstreamAlgorithm() : protocols::match::downstream::DownstreamAlgorithm
• DownstreamBuilder() : protocols::match::downstream::DownstreamBuilder
• DownstreamCoordinateKinemageWriter() : protocols::match::output::DownstreamCoordinateKinemageWriter
• DownstreamHitSets : protocols::match::output::CloudPDBWriter
• DownstreamRMSEvaluator() : protocols::match::output::DownstreamRMSEvaluator
• dp() : protocols::fldsgn::topology::DimerPairing
• dp_ : protocols::fldsgn::topology::DimerPairing
• DP_iter() : protocols::hybridization::TMalign
• dphi : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• dr_cycles() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• dr_cycles_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• drift() : protocols::simple_moves::GenericMonteCarloMover
• drift_ : protocols::protein_interface_design::movers::LoopOver , protocols::simple_moves::GenericMonteCarloMover
• drop_inter_group_edges() : protocols::simple_moves::GreenPacker
• drop_intra_group_edges() : protocols::simple_moves::GreenPacker
• drop_random_rate() : protocols::topology_broker::ConstraintClaimer
• drop_random_rate_ : protocols::topology_broker::ConstraintClaimer
• drop_rots_above_cutoff_ : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• drop_strand_pairs() : protocols::fldsgn::topology::StrandPairingSet
• drop_unsatisfied_voxels() : protocols::match::OccupiedSpaceHash
• dry_run() : protocols::relax::RelaxProtocolBase
• dry_run_ : protocols::match::upstream::FullChiSampleSet , protocols::relax::RelaxProtocolBase
• ds_atom_ids_needed_ : protocols::match::downstream::TargetRotamerCoords
• ds_atom_present() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• ds_builders_ : protocols::match::output::DownstreamRMSEvaluator
• ds_hitset_end_its() : protocols::match::output::CloudPDBWriter
• ds_hitset_end_its_ : protocols::match::output::CloudPDBWriter
• ds_hitset_its() : protocols::match::output::CloudPDBWriter
• ds_hitset_its_ : protocols::match::output::CloudPDBWriter
• dSASA : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dSASA_cutoff_ : protocols::features::InterfaceFeatures
• dSASA_fraction : protocols::analysis::PerResidueInterfaceData
• dSASA_sc : protocols::analysis::InterfaceData , protocols::analysis::PerResidueInterfaceData
• dsbuilder_ : protocols::match::downstream::DownstreamAlgorithm , protocols::match::output::SingleDownstreamResidueWriter
• dsbuilders() : protocols::match::output::PDBWriter
• dsbuilders_ : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::output::PDBWriter , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::UpstreamDownstreamCollisionFilter
• dscore_binding : protocols::dna::Reversion
• dscore_bound : protocols::dna::Reversion
• dsgn_boundary_ : protocols::flxbb::DesignTask_Layer
• dsgn_core_ : protocols::flxbb::DesignTask_Layer
• dsgn_surface_ : protocols::flxbb::DesignTask_Layer
• dspec_binding : protocols::dna::Reversion
• dspec_bound : protocols::dna::Reversion
• dspos : protocols::match::match_dspos1
• dspos1_mode() : protocols::match::output::BestMatchesCollection
• dspos1_mode_ : protocols::match::output::BestMatchesCollection
• dspose_ : protocols::match::output::DownstreamRMSEvaluator
• dssp : protocols::features::SecondaryStructureSegment
• Dssp : protocols::fldsgn::BluePrintBDR
• dssp_phi() : protocols::frag_picker::VallResidue
• dssp_phi_ : protocols::frag_picker::VallResidue
• dssp_psi() : protocols::frag_picker::VallResidue
• dssp_psi_ : protocols::frag_picker::VallResidue
• dssp_updated_ss : protocols::forge::remodel::RemodelData
• DsspDesignOperation() : protocols::toolbox::task_operations::DsspDesignOperation
• DsspMover() : protocols::moves::DsspMover
• dsspSS_ : protocols::forge::remodel::RemodelMover::instruction_flags
• dswriter_ : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::output::WriteUpstreamHitKinemage
• dswriters_ : protocols::match::output::WriteKinemageOutputter
• dt() : protocols::md::MDBase
• dt_ : protocols::md::MDBase
• dt_ang_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• dtest_cutoff() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dtest_cutoff_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dtor_ : protocols::normalmode::TorsionNormalModeMover
• DualMonteCarlo() : protocols::moves::DualMonteCarlo
• dualspace() : protocols::relax::FastRelax
• dualspace_ : protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::relax::FastRelax
• dummy_modify() : protocols::forge::build::BuildManager
• dummy_pose_ : protocols::sic_dock::NoPoseXYX_Func
• dummy_score_variations_ : protocols::jd2::archive::EvaluatedArchive
• DummyClass() : protocols::toolbox::DummyClass
• dump() : protocols::checkpoint::FileBuffer , protocols::electron_density::BfactorMultifunc , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::normalmode::NormalModeMultifunc , protocols::pockets::FingerprintMultifunc , protocols::pockets::PocketExemplarMultifunc , protocols::qsar::qsarOptFunc , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• dump_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• dump_BRIX() : protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid
• dump_conformer() : protocols::ligand_docking::Transform
• dump_debug_pdb() : protocols::scoring::ImplicitFastClashCheck
• dump_decoy_or_score() : protocols::canonical_sampling::CanonicalSamplingMover
• dump_eggshell() : protocols::pockets::EggshellGrid
• dump_file() : protocols::simple_filters::EvaluatedTrialMover
• dump_invrots_tree_as_multimodel_pdbs() : protocols::toolbox::match_enzdes_util::InvrotTree
• dump_jump_log() : protocols::abinitio::KinematicAbinitio
• dump_linkers() : protocols::sic_dock::LinkerScore
• dump_loops_only_ : protocols::canonical_sampling::CanonicalSamplingMover
• dump_matching_motifs() : protocols::sic_dock::scores::MotifHashRigidScore
• dump_minimal_pdb() : protocols::sic_dock::Rose
• dump_motif_hit() : protocols::motifs::MotifHit
• dump_motifs_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dump_oriented_pose_and_fp_to_pdb() : protocols::pockets::PlaidFingerprint
• dump_packertask() : protocols::flxbb::DesignTask
• dump_PCS_info() : 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
• dump_pdb() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::protein_interface_design::filters::FilterScanFilter , protocols::sic_dock::Rose
• dump_pdb_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::farna::RNA_DeNovoProtocol , protocols::hybridization::CartesianSampler , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::protein_interface_design::filters::FilterScanFilter
• dump_pdb_name() : protocols::protein_interface_design::filters::FilterScanFilter
• dump_pdb_name_ : protocols::protein_interface_design::filters::FilterScanFilter
• dump_pdb_tag_ : protocols::hybridization::CartesianSampler
• dump_pdb_to_file() : protocols::helix_capper::HelixNCapperMover , protocols::vip::VIP_Mover
• dump_pdb_when_fail() : protocols::fldsgn::BluePrintBDR
• dump_pdb_when_fail_ : protocols::fldsgn::BluePrintBDR
• dump_pdbs() : protocols::ddg::ddGMover , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• dump_pdbs_ : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• dump_pose() : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::PDBJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• dump_pose_ : protocols::cryst::TagPoseWithRefinementStatsMover
• dump_pose_and_map() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor
• dump_pose_fname() : protocols::simple_filters::RelativePoseFilter
• dump_pose_fname_ : protocols::simple_filters::RelativePoseFilter
• dump_poses() : protocols::md::CartesianMD
• dump_pymol() : protocols::jumping::JumpSample
• dump_rounds_ : protocols::mpi_refinement::MPI_Refine_Emperor
• dump_scores() : protocols::jobdist::PlainPdbJobDistributor
• dump_scoring_table() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• dump_silent() : protocols::jobdist::PlainSilentFileJobDistributor
• dump_snapshots_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• dump_structures() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine
• dump_table() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• dump_table_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::simple_filters::NMerSVMEnergyFilter
• dump_trisbpy() : protocols::sic_dock::scores::TrisBpyScore
• dump_weights() : protocols::noesy_assign::PeakAssignment
• dump_weights_file_ : protocols::abinitio::LoopJumpFoldCst
• dump_xtc_format_decoy() : protocols::canonical_sampling::CanonicalSamplingMover
• dumpall_ : protocols::relax::FastRelax
• dumpExemplars_ : protocols::pockets::PocketGrid
• dumpExemplarToFile() : protocols::pockets::PocketGrid
• dumpfile_ : protocols::matdes::SchemePlaceMotifsMover
• dumpGridToFile() : protocols::pockets::PocketGrid
• DumpPdb() : protocols::simple_moves::DumpPdb
• dumppdb_ : protocols::pockets::PocketConstraint
• dumpPDB_abinitio : protocols::flexpep_docking::FlexPepDockingFlags
• dumpPDB_hires : protocols::flexpep_docking::FlexPepDockingFlags
• dumpPDB_lowres : protocols::flexpep_docking::FlexPepDockingFlags
• dumpTargetPocketsToFile() : protocols::pockets::PocketGrid
• dumpTargetPocketsToPDB() : protocols::pockets::PocketGrid , protocols::pockets::TargetPocketGrid
• dunbrack_accept() : protocols::simple_moves::sidechain_moves::SidechainMover
• DunbrackRotamerSampleData : protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::ProteinSCSampler , protocols::match::upstream::ProteinUpstreamBuilder
• DunbrackRotamerSampleDataVector : protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::ProteinSCSampler , protocols::match::upstream::ProteinUpstreamBuilder
• DunbrackSCSampler() : protocols::match::upstream::DunbrackSCSampler
• duplicate_residues_by_type() : protocols::simple_moves::RepeatPropagationMover
• dynamic_grid_refinement() : protocols::match::MatcherTask
• dynamic_grid_refinement_ : protocols::match::Matcher , protocols::match::MatcherTask
• DynamicAggregateFunction() : protocols::pack_daemon::DynamicAggregateFunction
• dz1_initial_ : protocols::helical_bundle::FitSimpleHelix