- d -

• d : protocols::simple_moves::MinimalRotamer
• d0 : protocols::hybridization::TMalign
• d0_ : core::scoring::TMscore
• D0_MIN : protocols::hybridization::TMalign
• d0_out_ : protocols::hybridization::TMalign
• d0_search : protocols::hybridization::TMalign
• d0_search_ : core::scoring::TMscore
• d0A : protocols::hybridization::TMalign
• d0B : protocols::hybridization::TMalign
• d12_ : protocols::toolbox::match_enzdes_util::LigandConformer
• d1_ : core::scoring::FACTSRsdTypeInfo
• d2 : protocols::normalmode::ContactStruct
• d23_ : protocols::toolbox::match_enzdes_util::LigandConformer
• d2_ : core::scoring::FACTSRsdTypeInfo
• D2_ : core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainTripleFunc
• d2_low_ : core::scoring::lkball::LK_BallEnergy
• d2target_ : protocols::jumping::ChainbreakDistFunc
• D3_ : core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainTripleFunc
• D4_ : core::scoring::func::GaussianChainQuadrupleFunc
• 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_ : core::chemical::AddConnect , core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::ResetBondLength , core::chemical::SetICoor , core::kinematics::tree::BondedAtom , core::scoring::carbohydrates::CHIEnergyFunction
• D_ : core::scoring::ResidualDipolarCoupling
• d_ : protocols::scoring::methods::saxs::PDDFEnergy
• d_aa_set_ : core::io::NomenclatureManager
• d_location : core::scoring::disulfides::FullatomDisulfideParams13
• d_mean : core::scoring::sc::_RESULTS
• d_median : core::scoring::sc::_RESULTS
• d_scale : core::scoring::disulfides::FullatomDisulfideParams13
• d_shape : core::scoring::disulfides::FullatomDisulfideParams13
• d_to_l_mapping_ : core::chemical::ResidueTypeSet
• dada : core::scoring::packstat::Circle
• daemon_poses_ : protocols::pack_daemon::DaemonSet
• daemon_set_ : protocols::pack_daemon::MultistateFitnessFunction
• daemon_tasks_ : protocols::pack_daemon::DaemonSet
• daemons_ : 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
• DATA : protocols::sparta::GDB
• data_ : core::fragment::FragData , core::graph::UEEdge< V, E > , core::graph::UEVertex< V, E > , core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::pack::rotamer_set::WaterPackingInfo , core::scoring::func::CircularGeneral1D_Func , core::scoring::methods::D2H_SA_Energy , 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_annotations_ : core::io::rna::RDAT
• data_cache_ : core::conformation::Residue , core::conformation::RotamerSetBase , core::pose::Pose , core::scoring::Energies , core::scoring::ResPairMinimizationData , core::scoring::ResSingleMinimizationData
• DATA_DELIMETER : protocols::denovo_design::components::StructureData
• data_filename_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• data_format_ : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• data_in_fft : core::scoring::fiber_diffraction::Hankel
• data_int_ : protocols::denovo_design::components::StructureData
• data_line : core::scoring::rna::chemical_shift::ChemicalShiftData
• data_map_ : protocols::qsar::qsarOptFunc
• DATA_NAME : protocols::denovo_design::components::StructureData
• data_ndx_ : protocols::toolbox::KClusterElement
• data_real_ : protocols::denovo_design::components::StructureData
• data_source_ : protocols::toolbox::task_operations::ConservativeDesignOperation
• data_str_ : protocols::denovo_design::components::StructureData
• database_ : core::scoring::hbonds::HBondEnergy
• database_directory_ : core::chemical::ResidueTypeSet
• database_filter_ : protocols::features::ProteinSilentReport
• 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::loops::loops_definers::LoopsDatabaseDefiner , protocols::toolbox::task_operations::ReadResfileFromDB
• dataloader_creator_map_ : protocols::jd2::parser::DataLoaderFactory
• datamap_ : protocols::frag_picker::frag_movers::FragSetFromH5Mover
• dataset_ : protocols::toolbox::KClusterData
• db_ : core::scoring::methods::CartesianBondedEnergy , protocols::features::ProteinBondGeometryFeatures
• db_ang_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• db_base_path_ : protocols::antibody::constraints::CDRDihedralConstraintMover
• dB_dBdnmtr_ : core::scoring::FACTSResidueInfo
• dB_dBnmtr_ : core::scoring::FACTSResidueInfo
• db_disulfides_ : core::scoring::disulfides::DisulfideMatchingDatabase
• 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_init_ : core::scoring::disulfides::DisulfideMatchingDatabase
• 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::antibody::AntibodyDatabaseManager , protocols::features::ReportToDB , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::rotamer_recovery::RRReporterSQLite , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::trajectory::DbTrajectoryReader , protocols::wum::DatabaseEntryWorkUnit
• dbg : core::scoring::APBSConfig
• dbg_output_ : protocols::ddg::ddGMover
• dBR_ : core::pack::interaction_graph::FASTERInteractionGraph
• dBR_dG_ : core::scoring::FACTSResidueInfo
• dbx : core::scoring::APBSResult
• dby : core::scoring::APBSResult
• dbz : core::scoring::APBSResult
• dc_score_ : core::scoring::methods::DipolarCouplingEnergy
• dcalibrate_ : protocols::noesy_assign::PeakAssignmentParameters , protocols::noesy_assign::StructureDependentPeakCalibrator
• dCCdxs_aacen : core::scoring::electron_density::ElectronDensity
• dCCdxs_cen : core::scoring::electron_density::ElectronDensity
• dCCdxs_pat : core::scoring::electron_density::ElectronDensity
• dCCdxs_res : core::scoring::electron_density::ElectronDensity
• DCerr_ : core::scoring::DC
• dchi2_d : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• dchi2_d_cross_R : core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• dchi2_dca : core::scoring::saxs::FastSAXSEnergy
• dchi2_dsc : core::scoring::saxs::FastSAXSEnergy
• dchidevpen_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchidevpen_dchi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchimean_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchimean_domg_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchisd_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchisd_domg_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dCOM_ : protocols::constraints_additional::COMCoordinateConstraint
• dcs_kappa1 : core::scoring::disulfides::FullatomDisulfideParams13
• dcs_kappa2 : core::scoring::disulfides::FullatomDisulfideParams13
• dcs_kappa3 : core::scoring::disulfides::FullatomDisulfideParams13
• dcs_logA1 : core::scoring::disulfides::FullatomDisulfideParams13
• dcs_logA2 : core::scoring::disulfides::FullatomDisulfideParams13
• dcs_logA3 : core::scoring::disulfides::FullatomDisulfideParams13
• dcs_mu1 : core::scoring::disulfides::FullatomDisulfideParams13
• dcs_mu2 : core::scoring::disulfides::FullatomDisulfideParams13
• dcs_mu3 : core::scoring::disulfides::FullatomDisulfideParams13
• dcu0 : protocols::hybridization::TMalign
• dcut_ : protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::PeakAssignmentParameters
• DCval_ : core::scoring::DC
• DCval_computed_ : core::scoring::DC
• ddg_ : protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::seeded_abinitio::GrowPeptides
• ddg_based_ : protocols::seeded_abinitio::SeedFoldTree
• 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_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
• ddg_threshold_ : protocols::simple_filters::DdgFilter
• ddG_threshold_ : protocols::simple_filters::RotamerBoltzmannWeight
• ddg_tolerance_ : protocols::protein_interface_design::Revert
• ddGs_ : protocols::optimize_weights::IterativeOptEDriver , protocols::simple_filters::RotamerBoltzmannWeight
• ddGs_binding_ : protocols::optimize_weights::IterativeOptEDriver
• 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
• DDP_lookup_table_ : core::scoring::ScoringManager
• dE_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_dev_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_dev_perchi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_rot_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_semi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_dev_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_semi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• 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
• dec15_score : core::scoring::packing::HolesResult
• 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
• decompose_bb_hb_into_pair_energies_ : core::scoring::hbonds::HBondOptions
• decoy_compatibility_ : protocols::noesy_assign::PeakAssignment
• decoy_count_ : protocols::boinc::Boinc
• decoy_discrim_data_ : protocols::optimize_weights::IterativeOptEDriver
• decoy_loop_cutpoint_ : protocols::antibody_legacy::CDRH3Modeler
• decoy_params_ : core::scoring::packing::HolesEnergy
• decoy_score : core::scoring::packing::HolesResult
• decoy_tag_ : core::io::raw_data::RawStruct , core::io::silent::SilentStruct
• decoys_ : protocols::jd2::archive::ArchiveBase , protocols::optimize_weights::PNatStructureOptEData , protocols::wum::WorkUnit_SilentStructStore
• decoys_returned_to_archive_ : protocols::jd2::archive::Batch
• deep_optimization_ : protocols::antibody::GraftedStemOptimizer
• def_parameters : protocols::relax::CentroidRelax
• dEfac_ : core::scoring::etable::coulomb::Coulomb
• default_allow_bondangles_ : protocols::helical_bundle::MakeBundle
• default_allow_bondangles_set_ : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths_ : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths_set_ : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals_ : 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 : core::scoring::PoissonBoltzmannPotential , protocols::pb_potential::SetupPoissonBoltzmannPotential
• default_bias_ : protocols::canonical_sampling::BiasEnergy
• default_commands_ : core::pack::task::ResfileContents
• default_crick_params_file_ : 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_set_ : protocols::helical_bundle::MakeBundle
• default_delta_omega1_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::PerturbBundle
• default_delta_omega1_all_ : 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_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_set_ : protocols::helical_bundle::MakeBundle
• default_invert_ : protocols::helical_bundle::MakeBundle
• default_invert_set_ : protocols::helical_bundle::MakeBundle
• default_omega0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_omega0_set_ : protocols::helical_bundle::MakeBundle
• default_omega1_ : protocols::helical_bundle::MakeBundle
• default_omega1_set_ : protocols::helical_bundle::MakeBundle
• default_position : core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow
• default_precision_ : protocols::frag_picker::scores::FragmentScoreManager
• default_r0_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_r0_set_ : protocols::helical_bundle::MakeBundle
• default_rama_table_type_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• default_repeating_unit_offset_ : protocols::helical_bundle::MakeBundle
• default_repeating_unit_offset_set_ : protocols::helical_bundle::MakeBundle
• default_repeats_ : protocols::relax::FastRelax
• default_residue_name_ : 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_ : core::id::AtomID_Map< T > , core::id::NamedAtomID_Map< T > , protocols::helical_bundle::PerturbBundleOptions
• default_variant_ : core::scoring::MultipoleElecPotential , core::scoring::VdWTinkerPotential
• default_weight_ : core::pack::task::IGEdgeReweighter
• 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_set_ : 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_set_ : protocols::helical_bundle::MakeBundle
• default_z1_set_ : protocols::helical_bundle::MakeBundle
• define_match_by_single_downstream_positioning_ : protocols::match::MatcherTask
• defined_adducts_ : core::chemical::ResidueType
• definition_threshold_ : protocols::features::HBondFeatures
• definition_type_ : protocols::features::HBondFeatures
• degeneracy : core::chemical::rings::RingConformer
• degenerate_conformers_ : core::chemical::rings::RingConformerSet
• 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_checkpoints_ : protocols::checkpoint::CheckPointer
• delete_content_only_ : protocols::simple_filters::FileRemoveFilter
• delete_interface_native_sidechains_ : protocols::anchored_design::AnchoredDesignMover
• delete_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• delete_probability_ : protocols::sewing::MonteCarloAssemblyMover
• delete_res_range_list_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• delete_virtual_residues_after_FastRelax_ : protocols::relax::FastRelax
• deleted_ : core::graph::UEEdge< V, E >
• delR_ : protocols::electron_density::DockIntoDensityMover
• delta : protocols::moves::TrialMover
• delta2max : core::pose::rna::RNA_SuiteName
• delta2min : core::pose::rna::RNA_SuiteName
• delta3max : core::pose::rna::RNA_SuiteName
• delta3min : core::pose::rna::RNA_SuiteName
• delta_ : protocols::dna::DNABase , protocols::moves::IteratedConvergenceMover , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::LoopLengthChange , 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_atom_names_ : core::scoring::dna::DNATorsionPotential
• delta_atr_score_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_components_ : core::scoring::dna::DNATorsionPotential
• delta_coms : protocols::simple_filters::SymmetricMotifFilter
• delta_cutoff : core::pose::rna::RNA_SuiteName
• delta_cutoff_ : core::chemical::rna::RNA_FittedTorsionInfo , core::pose::rna::RNA_IdealCoord
• DELTA_CUTOFF_ : core::scoring::dna::DNATorsionPotential
• delta_energies_unweighted_ : core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator
• delta_fade_ : core::scoring::rna::RNA_TorsionPotential
• delta_filter_thresholds_ : 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_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• delta_omega0_ : protocols::helical_bundle::BundleGridSampler , 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::parameters::BundleParameters
• delta_omega1_guesses_ : protocols::helical_bundle::FitSimpleHelix
• delta_omega1_vals_output_ : protocols::helical_bundle::FitSimpleHelix
• delta_rep_score_ : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker , protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker
• delta_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• delta_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• delta_t_ : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_unsat_hbonds : protocols::analysis::InterfaceData
• delta_z1_ : protocols::helical_bundle::parameters::BundleParameters
• delta_z1_guesses_ : protocols::helical_bundle::FitSimpleHelix
• delta_z1_vals_output_ : protocols::helical_bundle::FitSimpleHelix
• deltaE_for_substitution_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G >
• deltaE_threshold_for_avoiding_hpatch_calcs_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• deltaE_threshold_for_avoiding_surface_calcs_ : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• deltaG_bind_ : protocols::optimize_weights::DGBindOptEData
• deltaT_ : protocols::canonical_sampling::BiasEnergy
• denovo_scorefxn_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol , protocols::farna::RNA_FragmentMonteCarlo
• dens_max : core::scoring::electron_density::ElectronDensity
• dens_mean : core::scoring::electron_density::ElectronDensity
• dens_min : core::scoring::electron_density::ElectronDensity
• dens_stdev : core::scoring::electron_density::ElectronDensity
• dens_wt_ : protocols::electron_density::DockIntoDensityMover
• density : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise , core::scoring::sc::Atom , core::scoring::sc::MolecularSurfaceCalculator , protocols::simple_moves::ThermodynamicData
• density_redraw : protocols::viewer::GraphicsState
• density_sigma : protocols::viewer::GraphicsState
• densityPtr : protocols::viewer::triangleIterator
• dentropy_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dep_day_ : core::io::HeaderInformation
• dep_month_ : core::io::HeaderInformation
• dep_year_ : core::io::HeaderInformation
• dependencies_ : protocols::forge::build::BuildInstruction
• dependent_ : core::optimization::DOF_Node
• dependent_dof_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• dependent_dof_nodes_ : core::optimization::symmetry::SymMinimizerMap
• dependent_node_map_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• dependent_residue_map_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• depth_ : core::optimization::DOF_Node , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , protocols::viewer::triangle
• deriv_ : core::scoring::rna::RNA_SuitePotential
• deriv_check_ : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::MinimizerOptions , core::optimization::symmetry::SymAtomTreeMultifunc , protocols::electron_density::BfactorFittingMover , protocols::electron_density::BfactorMultifunc , protocols::farna::options::RNA_MinimizerOptions , protocols::normalmode::NormalModeMultifunc
• deriv_check_result_ : core::optimization::AtomTreeMinimizer , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMinimizer , core::optimization::CartesianMultifunc , protocols::normalmode::NormalModeMinimizer , protocols::normalmode::NormalModeMultifunc
• deriv_check_results_ : core::optimization::NumericalDerivCheckResult
• deriv_check_to_stdout_ : core::optimization::MinimizerOptions
• deriv_check_verbose_ : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::MinimizerOptions , core::optimization::symmetry::SymAtomTreeMultifunc , protocols::normalmode::NormalModeMultifunc
• deriv_cutoff_ : core::optimization::BrentLineMinimization
• deriv_phi_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• deriv_psi_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• deriv_type2name_ : core::scoring::hbonds::HBondTypeManager
• derivative_atom_types_ : core::scoring::disulfides::DisulfideAtomIndices
• derivative_graph_ : core::scoring::symmetry::SymmetricEnergies
• derivs_ : core::scoring::hbonds::HBond
• derivs_of_ray_distances_ : protocols::pockets::PlaidFingerprint
• descriptors_ : protocols::features::ScreeningFeatures
• design_ : protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions , protocols::cryst::DockLatticeMover , 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_antigen_ : protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• design_cdrs_ : protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• design_chain1_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chain2_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chains_ : protocols::docking::DockTaskFactory
• design_disabled_ : core::pack::task::ResidueLevelTask_
• design_enum_manager_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::CDRSeqDesignOptionsParser
• design_foldpose_ : protocols::seeded_abinitio::SeedSetupMover
• design_framework_ : protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• design_framework_conservative_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_framework_conserved_res_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_h3_stem_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_info_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• design_layer_ : protocols::flxbb::LayerDesignOperation
• design_loops_ : protocols::toolbox::task_operations::RestrictToLoops
• design_matrix : protocols::forge::remodel::RemodelWorkingSet
• design_mode : protocols::forge::remodel::RemodelData
• 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_only_target_residues_ : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• design_override_ : protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyDesignProtocol
• design_partner1_ : protocols::simple_moves::DesignRepackMover
• design_partner2_ : protocols::simple_moves::DesignRepackMover
• design_peptide : protocols::flexpep_docking::FlexPepDockingFlags
• design_proline_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_protocol_ : protocols::antibody::design::AntibodyDesignMover
• design_protocol_to_enum_ : protocols::antibody::design::AntibodyDesignEnumManager
• design_protocol_to_string_ : protocols::antibody::design::AntibodyDesignEnumManager
• design_res_ : protocols::seeded_abinitio::SeedSetupMover
• design_shell_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::toolbox::task_operations::DesignAroundOperation
• design_strategy_ : protocols::antibody::design::CDRSeqDesignOptions
• design_target_ : protocols::seeded_abinitio::SeedSetupMover
• design_target_res_ : protocols::enzdes::DetectProteinLigandInterface
• design_targets_ : protocols::enzdes::EnzdesBaseProtocol , protocols::enzdes::EnzdesFlexibleRegion
• design_taskset_ : protocols::flxbb::FlxbbDesign
• design_type : protocols::forge::remodel::LineObject
• designable : protocols::dna::PositionType
• designable_ : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::toolbox::task_operations::DatabaseThread
• designable_only_ : 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
• designed_residues_ : protocols::dna::PDBOutput
• designing_ : core::pack::task::ResidueLevelTask_
• desired_conformer_ : protocols::enzdes::ResidueConformerFilter
• desired_entity_history_size_ : protocols::pack_daemon::TopEntitySet
• desired_remodel_ss_strings_ : protocols::enzdes::EnzdesFlexibleRegion
• desired_remodelres_in_vicinity_ : protocols::forge::remodel::ResidueVicinityInfo
• desired_result_ : core::chemical::ResidueTypeSelectorSingle
• desired_sequence_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• desired_ss_chars_ : protocols::match::SecondaryStructureMPM
• destruction_obs_hub_ : core::pose::Pose
• desymmeterize_ : protocols::match::upstream::DunbrackSCSampler
• detach_after_modify_ : protocols::forge::build::BuildInstruction
• detailed_balance_ : protocols::canonical_sampling::CanonicalSamplingMover
• details : update_ResidueType_enum_files.EnumInfo
• detect_bonds_ : protocols::simple_moves::DeleteChainsMover
• detect_design_interface_ : protocols::enzdes::DetectProteinLigandInterface
• detect_pseudobonds_ : protocols::simple_moves::DeleteChainsMover
• deviation_ : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• dfade_max_ : core::scoring::hbonds::FadeInterval
• dfade_min_ : core::scoring::hbonds::FadeInterval
• 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_dCi_ : core::scoring::FACTSResidueInfo
• dG_dSASA_ratio : protocols::analysis::InterfaceData
• dhist_ : core::scoring::saxs::SAXSEnergy
• DHO_Haro_scOrbH_splines_ : core::scoring::orbitals::OrbitalsLookup
• DHO_Hpol_bbOrbH_splines_ : core::scoring::orbitals::OrbitalsLookup
• DHO_Hpol_scOrbH_splines_ : core::scoring::orbitals::OrbitalsLookup
• 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
• Di_ : core::scoring::FACTSResidueInfo
• die_ : core::scoring::etable::coulomb::Coulomb
• diff_torsions : protocols::stepwise::modeler::rna::output_data_struct
• dihedral_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• dihedral_atom_sets_ : core::chemical::ResidueType
• dihedral_constraint_energy_ : core::scoring::constraints::ConstraintEdge
• dihedral_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• dihedral_cst_weight_ : protocols::antibody::AntibodyCDRGrafter
• dihedral_max_ : protocols::ncbb::SecStructFinder
• dihedral_min_ : protocols::ncbb::SecStructFinder
• dihedral_pattern_ : protocols::ncbb::SecStructFinder , protocols::ncbb::SecStructMinimizeMover , protocols::ncbb::SecStructMinimizeMultiFunc
• dihedral_sampling_data_ : core::scoring::carbohydrates::CHIEnergyFunction
• dihedrallist : protocols::cartesian::MolecularDynamics
• dihedrals_ : protocols::ncbb::SecStructMinimizeMover
• dihedrals_for_atom_ : core::chemical::ResidueType
• dim_ : protocols::pockets::PocketGrid , protocols::toolbox::ClusterBase
• dim_prods_ : protocols::match::OccupiedSpaceHash
• dime : core::scoring::APBSConfig
• dimer1_ : core::scoring::DimerPairing
• dimer2_ : core::scoring::DimerPairing
• dimer_neighbor : core::scoring::Strands
• dimer_seqsep_cutoff_ : protocols::fldsgn::potentials::sspot::SSPairPotential
• dimprods_ : protocols::match::Bool3DGrid
• dimsizes_ : protocols::match::Bool3DGrid
• dip_score_ : core::scoring::methods::ResidualDipolarCouplingEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• dipole_ : core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleParameter
• dir_ : protocols::rigid::RigidBodyMover
• direction : protocols::hotspot_hashing::VectorPair
• direction_ : protocols::normalmode::NormalModeRelaxMover
• directory_ : core::chemical::AtomTypeSet , core::chemical::orbitals::OrbitalTypeSet , protocols::ligand_docking::WriteLigandMolFile
• dis2_step_ : core::scoring::etable::TableLookupEvaluator
• 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_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• disAB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• disable_packing_and_design_ : protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation
• disable_sampling_of_loop_takeoff_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• disabled_ : core::pack::task::ResidueLevelTask_ , protocols::checkpoint::CheckPointer , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• disallow_bps_at_extra_min_res_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• disallow_carboxyl_conjugation_at_glu_asp_ : core::chemical::ResidueTypeFinder
• disallow_deletion_of_last_residue_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• disallow_properties_ : core::chemical::ResidueTypeFinder
• disallow_quench_ : core::pack::annealer::SimAnnealerBase , core::pack::task::PackerTask_ , protocols::toolbox::task_operations::ModifyAnnealer
• disallow_realign_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• disallow_variants_ : core::chemical::ResidueTypeFinder
• disallowed_aas_ : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT
• disallowed_host_pos_ : protocols::protein_interface_design::movers::PlaceStubMover
• disallowed_pairs_ : protocols::denovo_design::connection::Connection
• disallowed_resids_ : core::pack::task::operation::OptH
• disallowed_value_ : protocols::flxbb::FilterStructs_TotalCharge
• discard_jumps_ : protocols::topology_broker::FragmentJumpClaimer
• dissimilarity_ : protocols::ncbb::SecStructFinder
• dist : core::pose::rna::RNA_SuiteAssignment , protocols::pockets::UnionEdge
• dist2_cut_ : protocols::normalmode::NormalMode
• dist_ : protocols::fldsgn::SheetConstraintGenerator , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::forge::constraints::NtoCConstraintGenerator
• dist_cut2_ : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• dist_cutoff_ : core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::toolbox::CalcInterNeighborGroup , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• dist_exponent_ : core::select::util::SelectResiduesByLayer
• dist_fade_ : core::scoring::rna::data::RNA_DataBackboneEnergy
• dist_list_ : protocols::toolbox::KClusterElement
• dist_midpoint_ : core::select::util::SelectResiduesByLayer
• dist_pow_ : core::pose::rna::RNA_SuiteName
• dist_sigma2_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• dist_squared_ : protocols::frag_picker::Contact , protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• dist_tolerance_ : protocols::fldsgn::SheetConstraintGenerator
• dist_track_ : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• dist_wts_ : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential
• distal_partition_res_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• distance : core::scoring::sc::_RESULTS , protocols::antibody::CDRDBPose , protocols::antibody::CDRDBSequence
• distance_ : core::chemical::Bond , core::chemical::orbitals::ICoorOrbitalData , core::chemical::orbitals::OrbitalType , core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::select::residue_selector::NeighborhoodResidueSelector , protocols::antibody::clusters::CDRCluster , protocols::contact_map::Contact , protocols::nonlocal::SheetTranslate , protocols::scoring::InterfaceInfo , protocols::sewing::Model , 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_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• distance_cutoff_ : core::select::residue_selector::NumNeighborsSelector , protocols::contact_map::ContactMap , protocols::features::ChargeChargeFeatures , protocols::features::ModelFeatures , 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
• distance_matrix_ : protocols::contact_map::ContactMap
• distance_pair_ : protocols::simple_moves::symmetry::SetupNCSMover
• distance_range_ : protocols::sewing::NodeConstraint
• distance_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• distance_squared : core::scoring::etable::AtomPairEnergy
• distance_squared_ : protocols::scoring::Interface
• distance_table_ : core::scoring::methods::GoapEnergy
• 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
• distanceFromStart : protocols::toolbox::Node
• distances_ : core::chemical::RigidDistanceVisitor
• distbin_map_ : core::scoring::methods::GoapEnergy
• disth : protocols::kinmatch::KRSQuery
• distinguish_backbone_and_sidechain_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• distinguish_pucker_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• distribute_over_mpi_ : protocols::optimize_weights::OptEMultifunc
• distribution : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Translate_info
• distribution_map_ : protocols::ligand_docking::DistributionMap
• distThresh_ : protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter
• disulf1_ : protocols::denovo_design::connection::ConnectTerminiWithDisulfide
• disulf2_ : protocols::denovo_design::connection::ConnectTerminiWithDisulfide
• disulf_atom_index_ : core::scoring::disulfides::DisulfideAtomIndices
• disulf_energy_cutoff_postrelax_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• disulf_energy_cutoff_prerelax_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• disulf_fa_max_ : protocols::forge::remodel::RemodelMover
• disulf_file_ : protocols::hybridization::HybridizeProtocol
• disulf_ssdist_cutoff_ : core::scoring::disulfides::FullatomDisulfidePotential
• disulfide_atom_indices_ : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• disulfide_atom_name_ : core::chemical::ResidueType
• disulfide_cb_dist_cutoff : core::scoring::disulfides::CentroidDisulfidePotential
• disulfide_cutpoint : protocols::forge::remodel::RemodelWorkingSet
• disulfide_data_ : protocols::frag_picker::scores::DisulfideDistance
• disulfide_file_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• disulfide_index_ : core::scoring::disulfides::CentroidDisulfideNeighborConstIterator , core::scoring::disulfides::CentroidDisulfideNeighborIterator , core::scoring::disulfides::DisulfideMatchingNeighborConstIterator , core::scoring::disulfides::DisulfideMatchingNeighborIterator , core::scoring::disulfides::DisulfResNeighbConstIterator , core::scoring::disulfides::DisulfResNeighbIterator
• disulfide_info_ : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• disulfide_jump_points : protocols::forge::remodel::RemodelWorkingSet
• disulfide_matching_potential_ : core::scoring::ScoringManager
• disulfide_partners_ : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• disulfide_residue_types_ : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• disulfide_ss : protocols::forge::remodel::RemodelWorkingSet
• disulfides_ : core::io::raw_data::DisulfideFile , protocols::simple_moves::ForceDisulfidesMover
• disulfLandingRange : protocols::forge::remodel::RemodelData
• disulfMobileRange : protocols::forge::remodel::RemodelData
• disulfs_ : protocols::hybridization::MRMover
• diversify_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• diversify_loop_only_ : protocols::loophash::LoopHashDiversifier
• djs_id_2_hphobe_index_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• djs_rep_node_index_2_cc_index_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• dlazy_edge_vector_ : core::pack::interaction_graph::DoubleLazyInteractionGraph
• dle_flag_ : protocols::antibody::ModelCDRH3 , protocols::antibody_legacy::CDRH3Modeler
• dlig_mem_limit_ : core::pack::task::PackerTask_
• dlig_nmeg_limit_ : protocols::pack_daemon::DaemonSet
• dljatr_ : core::scoring::etable::Etable , core::scoring::etable::TableLookupEvaluator , core::scoring::rna::RNA_LJ_BaseEnergy
• dljrep_ : core::scoring::etable::Etable , core::scoring::etable::TableLookupEvaluator , core::scoring::rna::RNA_LJ_BaseEnergy
• dmatrix_ : protocols::scoring::methods::saxs::PDDFEnergy
• dme_threshold_ : protocols::simple_moves::DME_FilterMover
• dml_dx : core::scoring::cryst::XtalMLEnergy
• dmp_pdb_ : protocols::ddg::ddGMover
• DMS_low_resolution_potential_ : core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::data::RNA_DMS_LowResolutionPotential
• DMS_potential_ : core::scoring::rna::data::RNA_ChemicalMappingEnergy , core::scoring::rna::data::RNA_DMS_Potential
• DMS_potential_binding_energy_ : core::scoring::rna::data::RNA_DMS_Potential
• DMS_potential_is_bonded_ : core::scoring::rna::data::RNA_DMS_Potential
• DMS_potential_occ_ : core::scoring::rna::data::RNA_DMS_Potential
• DMS_stats_ : core::scoring::rna::data::RNA_DMS_Potential
• DMS_values_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential , core::scoring::rna::data::RNA_DMS_Potential
• dna_base_distance_constraints_ : core::scoring::dna::DNATorsionEnergy
• dna_base_positions_ : protocols::dna::DNAParameters
• DNA_base_potential_ : core::scoring::ScoringManager
• dna_chains_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface
• dna_design_ : protocols::motifs::MotifDnaPacker
• dna_dihedral_potential_ : core::scoring::ScoringManager
• dna_dr_potential_ : core::scoring::ScoringManager
• dna_env_pair_potential_ : core::scoring::ScoringManager
• dna_move_ : protocols::relax::FastRelax
• dna_neighbors_ : protocols::dna::DnaInterfaceFinder
• dna_packer_ : protocols::motifs::MotifDnaPacker
• dna_positions_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dna_sequences_ : protocols::dna::DnaInterfacePacker
• dna_sugar_close_constraints_ : core::scoring::dna::DNATorsionEnergy
• dna_torsion_constraints_ : core::scoring::dna::DNATorsionEnergy
• dna_torsion_potential_ : core::scoring::dna::DNATorsionEnergy , core::scoring::ScoringManager
• dnabform_ : core::scoring::ScoringManager
• dneglnrotprob_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dnmtr_ : core::scoring::FACTSResidueInfo
• do_add_delete_ : protocols::stepwise::monte_carlo::rna::RNA_AddDeleteMonteCarlo
• do_align_ : protocols::protein_interface_design::filters::RmsdSimpleFilter
• do_apprx_ : core::scoring::FACTSPotential
• do_chain_closure_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• do_checks_ : protocols::stepwise::modeler::align::StepWiseClusterer
• do_classic_intrares_ : core::scoring::etable::BaseEtableEnergy< Derived >
• do_close_loops_ : protocols::farna::RNA_FragmentMonteCarlo
• do_cter_insert_ : protocols::antibody::ModelCDRH3
• do_h3_modeling_ : protocols::antibody_legacy::CDRH3Modeler
• do_hardsphere_bump_check_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• do_minimize_ : protocols::simple_moves::CombinePoseMover , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• 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_write_resfile_of_sandwich_that_has_non_canonical_LR_ : protocols::features::strand_assembly::SandwichFeatures
• do_rama_check_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• do_refine_ : protocols::electron_density::DockIntoDensityMover
• do_remodel_ : protocols::denovo_design::connection::Connection
• do_rosetta_library_domain_check_ : protocols::farna::libraries::RNA_ChunkLibrary
• do_sanity_check_ : protocols::loophash::LoopHashLibrary
• 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
• DOA_orb_orb_splines_ : core::scoring::orbitals::OrbitalsLookup
• dock_chains_ : protocols::analysis::InterfaceAnalyzerMover
• dock_cycles_ : protocols::antibody::design::AntibodyDesignMover
• dock_design_filter_map_ : protocols::protein_interface_design::DockDesignFilterFactory
• dock_design_loop_num_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• dock_into_dens_strategy_ : protocols::electron_density::SetupForDensityScoringMover
• 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_protocol_ : protocols::antibody::RefineBetaBarrel
• dock_min_ : protocols::docking::DockingProtocol
• dock_min_dock_ : protocols::antibody::design::AntibodyDesignMover
• dock_pert_ : protocols::docking::DockingInitialPerturbation
• dock_post_graft_ : protocols::antibody::design::AntibodyDesignMover
• dock_ppk_ : protocols::docking::DockingPrepackProtocol , protocols::symmetric_docking::SymDockProtocol
• dock_scorefxn_ : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel
• dock_scorefxn_highres_ : protocols::antibody::AntibodyModelerProtocol
• dock_trials_ : protocols::enzdes::PredesignPerturbMover
• 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_constraint_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_frequency_ : protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions
• docking_ft_ : protocols::protein_interface_design::movers::SetAtomTree
• docking_high_ : protocols::symmetric_docking::SymDockProtocol
• docking_highres_mover_ : protocols::docking::DockingProtocol
• docking_highres_protocol_mover_ : protocols::docking::DockingHighResLegacy , protocols::symmetric_docking::SymDockingHiRes
• 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_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::GeneralAntibodyModeler , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_scorefxn_low_ : protocols::antibody::design::GeneralAntibodyModeler , protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_scorefxn_output_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• docking_scorefxn_pack_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• dof : protocols::sic_dock::CorrectionVisitor
• dof_ : protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofRandomizeMover , protocols::rigid::RigidBodyDofTransMover
• dof_change_propagates_to_younger_siblings_ : core::kinematics::tree::BondedAtom
• dof_changeset_ : core::kinematics::AtomTree
• dof_conformers_ : protocols::jumping::ResiduePairJump
• dof_constraints_ : core::scoring::constraints::ConstraintSet
• dof_deriv_1benmeths_ : core::scoring::MinimizationNode
• dof_deriv_2benmeths_ : core::scoring::MinimizationNode
• dof_id2torsion_id_ : core::optimization::symmetry::SymMinimizerMap
• dof_id_ : core::id::DOF_ID_Range , core::optimization::DOF_DataPoint , core::scoring::constraints::DOF_Constraint
• dof_id_map_ : core::kinematics::MoveMap
• 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_map_ : core::id::DOF_ID_Map< T >
• dof_mask_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• dof_moved_ : core::conformation::Conformation
• dof_node_pointer_ : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• dof_nodes_ : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap
• dof_refold_index_ : core::kinematics::tree::Atom_
• dof_sample_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• dof_samples_ : protocols::helical_bundle::BundleGridSamplerHelper
• dof_start_for_focused_residue_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• dof_step_data_ : core::optimization::NumDerivCheckData
• dof_tasks_ : protocols::simple_moves::MinMover
• dof_type_map_ : core::kinematics::MoveMap
• dof_upper_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• dof_val_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• dof_values_ : protocols::simple_moves::DOFHistogramRecorder
• dof_variables_ : protocols::optimize_weights::WrapperOptEMultifunc
• dofid_to_atoms_ : core::pack::scmin::CartSCMinMinimizerMap
• dofname2jnum_ : core::conformation::symmetry::SymmetryInfo
• dofs_ : core::conformation::symmetry::SymmData , core::conformation::symmetry::SymmetryInfo , 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::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• dofs_info_ : core::pose::copydofs::CopyDofsInfo
• domain_map : protocols::cartesian::MolecularDynamics
• domain_map_ : core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::Energies , core::scoring::NeighborList , protocols::toolbox::AtomLevelDomainMap
• domain_move_frequency_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• domain_visited_ : core::scoring::loop_graph::LoopGraph
• domains_all_templ_ : protocols::hybridization::HybridizeProtocol
• dominant_ : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• dominant_suites : core::pose::rna::RNA_SuiteName
• don_chem_type2name_ : core::scoring::hbonds::HBondTypeManager
• don_deriv : core::scoring::hbonds::HBondDerivs
• don_dist_cutoff_ : protocols::features::WaterFeatures
• don_hatm_ : core::scoring::hbonds::HBond
• don_hatm_is_backbone_ : core::scoring::hbonds::HBond
• don_hatm_is_protein_backbone_ : core::scoring::hbonds::HBond
• don_res_ : core::scoring::hbonds::HBond
• don_res_is_dna_ : core::scoring::hbonds::HBond
• don_res_is_protein_ : core::scoring::hbonds::HBond
• don_strength_lookup_ : core::scoring::hbonds::HBondDatabase
• don_type_ : core::scoring::hbonds::HBEvalTuple
• done_loading_ : core::scoring::motif::MotifHashManager
• donor_atom_xyz_list_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• donor_base_atom_xyz_list_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• donor_occ_data_ : core::scoring::geometric_solvation::DatabaseOccSolEne
• donor_structure_ : protocols::antibody::AntibodyCDRGrafter
• donorList : protocols::sparta::PDB
• donors : protocols::sic_dock::EdgeStandScore
• donors_ : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• dont_compute_cav_balls : core::scoring::packstat::SasaOptions
• dot_coords_ : core::pack::interaction_graph::RotamerDots
• dots : core::scoring::sc::_RESULTS , core::scoring::sc::MolecularSurfaceCalculator
• dots_coverage_count_ : core::pack::interaction_graph::DotSphere
• dotscore_ : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• double_lazy_ : protocols::toolbox::task_operations::SetIGTypeOperation
• double_lazy_ig_ : core::pack::task::PackerTask_
• double_mutant_scan_ : protocols::pmut_scan::PointMutScanDriver
• down_jump_atom_ : protocols::simple_filters::JumpEvaluator
• down_stub_ : protocols::simple_filters::JumpEvaluator
• downhill_accepts_ : protocols::moves::MoverStatistics
• 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::Matcher , protocols::match::MatcherTask
• downstream_builders_ : protocols::match::Matcher
• downstream_chains_ : protocols::analysis::InterfaceAnalyzerMover
• downstream_conf_id : protocols::match::match_dspos1
• downstream_conf_id_ : protocols::match::downstream_hit
• downstream_orientation_atoms_ : protocols::match::Matcher , protocols::match::MatcherTask
• downstream_pose_ : protocols::match::Matcher , protocols::match::MatcherTask , protocols::match::output::UpstreamDownstreamCollisionFilter
• downstream_pose_from_task_ : protocols::match::output::PDBWriter
• downstream_restype_ : protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• downstream_stub_atoms_ : core::fragment::DownJumpSRFD
• dp_ : protocols::fldsgn::topology::DimerPairing
• dphi : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• Dphi_ : core::scoring::func::KarplusFunc
• dr_cycles_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• drdz : core::scoring::packstat::Circle
• drift_ : protocols::protein_interface_design::movers::LoopOver , protocols::simple_moves::GenericMonteCarloMover
• drop_random_rate_ : protocols::topology_broker::ConstraintClaimer
• drop_rots_above_cutoff_ : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• drotprob_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dry_run_ : protocols::match::upstream::FullChiSampleSet , protocols::relax::RelaxProtocolBase
• ds_ : core::scoring::SecondaryStructurePotential
• ds_atom_ids_needed_ : protocols::match::downstream::TargetRotamerCoords
• ds_builders_ : protocols::match::output::DownstreamRMSEvaluator
• ds_hitset_end_its_ : protocols::match::output::CloudPDBWriter
• ds_hitset_its_ : protocols::match::output::CloudPDBWriter
• dSA_dDi_ : core::scoring::FACTSResidueInfo
• 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::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
• dshift2_bb_ : core::scoring::FACTSPotential
• dshift2_bs_ : core::scoring::FACTSPotential
• dshift2_saltbridge_ : core::scoring::FACTSPotential
• dshift2_sc_ : core::scoring::FACTSPotential
• dslf_ca_dih_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_cbs_ds_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_cs_ang_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_fa13_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_ss_dih_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_ss_dst_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslfc_ang_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_bb_dih_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cb_dih_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cb_dst_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cen_dst_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_rot_ : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dslfc_RT_ : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dslfc_trans_ : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dsolv1_ : core::scoring::etable::Etable , core::scoring::etable::MembEtable , core::scoring::lkball::LK_BallEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::LK_hack
• dsolv2_ : core::scoring::etable::MembEtable , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• dsolv_ : core::scoring::etable::Etable , core::scoring::etable::TableLookupEvaluator , core::scoring::membrane::FaMPSolvEnergy , core::scoring::methods::Fa_MbsolvEnergy
• dsolv_dBR_ : core::scoring::FACTSResidueInfo
• dspec_binding : protocols::dna::Reversion
• dspec_bound : protocols::dna::Reversion
• dspos : protocols::match::match_dspos1
• dspos1_mode_ : protocols::match::output::BestMatchesCollection
• dspose_ : protocols::match::output::DownstreamRMSEvaluator
• dsq_ : core::conformation::PointGraphEdgeData
• dsqr_ : core::scoring::EnergyEdge
• dss_kappa1 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_kappa2 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_logA1 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_logA2 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_mixed_kappa1 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_mixed_kappa2 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_mixed_logA1 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_mixed_logA2 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_mixed_mu1 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_mixed_mu2 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_mu1 : core::scoring::disulfides::FullatomDisulfideParams13
• dss_mu2 : core::scoring::disulfides::FullatomDisulfideParams13
• dssp : protocols::features::SecondaryStructureSegment , protocols::features::Segment , protocols::sewing::segment
• dssp_ : protocols::sewing::SewSegment
• dssp_codes_ : protocols::sewing::sampling::requirements::GlobalLengthRequirement
• dssp_phi_ : protocols::frag_picker::VallResidue
• dssp_psi_ : protocols::frag_picker::VallResidue
• dssp_secstruct_ : core::scoring::dssp::Dssp
• dssp_updated_ss : protocols::forge::remodel::RemodelData
• dsspSS_ : protocols::forge::remodel::RemodelMover::instruction_flags
• dsurf : core::scoring::packing::SurfVolDeriv
• dswriter_ : protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::output::WriteUpstreamHitKinemage
• dswriters_ : protocols::match::output::WriteKinemageOutputter
• dt_ : protocols::md::MDBase
• dt_ang_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• dtest_cutoff_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dtor_ : protocols::normalmode::TorsionNormalModeMover
• dualspace_ : protocols::relax::FastRelax
• dummy_ : core::scoring::dna::DNABFormPotential
• dummy_atomid_ : core::scoring::aa_composition_energy::SequenceConstraint
• dummy_deriv : core::scoring::rna::RNA_LowResolutionPotential
• dummy_distance : core::scoring::GenBornPotential
• dummy_distance_ : core::scoring::FACTSPotential
• dummy_pose_ : protocols::sic_dock::NoPoseXYX_Func
• dummy_radius : core::scoring::GenBornPotential
• dummy_radius_ : core::scoring::FACTSPotential
• dummy_sample_ : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• dummy_scale : core::scoring::GenBornPotential
• dummy_scale_ : core::scoring::FACTSPotential
• dummy_score_variations_ : protocols::jd2::archive::EvaluatedArchive
• dump_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• dump_every_ : protocols::simple_moves::PeriodicBoxMover
• dump_initial_results_ : protocols::indel::IndelOptimizationMover
• dump_loops_only_ : protocols::canonical_sampling::CanonicalSamplingMover
• dump_motifs_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dump_pdb_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::farna::options::RNA_BasicOptions , 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_tag_ : protocols::hybridization::CartesianSampler
• dump_pdb_when_fail_ : protocols::fldsgn::BluePrintBDR
• dump_pdbs_ : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• dump_pose_ : protocols::cryst::TagPoseWithRefinementStatsMover
• dump_pose_fname_ : protocols::simple_filters::RelativePoseFilter
• dump_rounds_ : protocols::mpi_refinement::MPI_Refine_Emperor
• dump_snapshots_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• dump_table_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::simple_filters::NMerSVMEnergyFilter
• dump_threshold_ : protocols::ncbb::SecStructFinder
• dump_weights_file_ : protocols::abinitio::LoopJumpFoldCst
• dumpall_ : protocols::relax::FastRelax
• dumpExemplars_ : protocols::pockets::PocketGrid
• dumpfile_ : protocols::matdes::SchemePlaceMotifsMover
• dumppdb_ : protocols::pockets::PocketConstraint
• dumpPDB_abinitio : protocols::flexpep_docking::FlexPepDockingFlags
• dumpPDB_hires : protocols::flexpep_docking::FlexPepDockingFlags
• dumpPDB_lowres : protocols::flexpep_docking::FlexPepDockingFlags
• dun02_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• dun10 : core::init::pre_talaris_2013_behavior_settings
• dvol : core::scoring::packing::SurfVolDeriv
• dw_dr_ : core::scoring::elec::FAElecContextData
• dwater_datom1_ : core::scoring::lkball::LKB_ResidueInfo
• dwater_datom2_ : core::scoring::lkball::LKB_ResidueInfo
• dwater_datom3_ : core::scoring::lkball::LKB_ResidueInfo
• dweight_ : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• dx : core::scoring::APBSResult , core::scoring::packstat::LR_AtomData , core::scoring::packstat::LR_MP_AtomData
• dx_filename_ : core::scoring::PoissonBoltzmannPotential
• dy : core::scoring::APBSResult , core::scoring::packstat::LR_AtomData , core::scoring::packstat::LR_MP_AtomData
• dynamic_grid_refinement_ : protocols::match::Matcher , protocols::match::MatcherTask
• dz : core::scoring::APBSResult
• dz1_initial_ : protocols::helical_bundle::FitSimpleHelix