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

- d -

• d() : core::chemical::Adduct , core::chemical::AtomICoor , 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
• d1() : core::scoring::FACTSRsdTypeInfo
• d12_ : protocols::toolbox::match_enzdes_util::LigandConformer
• d1_ : core::scoring::FACTSRsdTypeInfo
• d2() : core::scoring::FACTSRsdTypeInfo , 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
• D2H_SA_Energy() : core::scoring::methods::D2H_SA_Energy
• 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_aa_set_ : core::io::NomenclatureManager
• d_location : core::scoring::disulfides::FullatomDisulfideParams13
• d_mean : core::scoring::sc::_RESULTS
• d_median : core::scoring::sc::_RESULTS
• d_phi() : protocols::frag_picker::PhiPsiTalosIO
• d_psi() : protocols::frag_picker::PhiPsiTalosIO
• d_scale : core::scoring::disulfides::FullatomDisulfideParams13
• d_shape : core::scoring::disulfides::FullatomDisulfideParams13
• d_to_l_mapping_ : core::chemical::ResidueTypeSet
• DAB_SASA_POSE_INFO : core::pose::datacache::CacheableDataType
• DAB_SEV_POSE_INFO : core::pose::datacache::CacheableDataType
• dada : core::scoring::packstat::Circle
• 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
• damp_long_range() : core::scoring::etable::Etable
• 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() : core::conformation::RotamerSetBase , core::graph::UEEdge< V, E > , core::graph::UEVertex< V, E > , core::pose::Pose , core::scoring::Energies , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptEPositionData
• 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_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_int_ : protocols::denovo_design::components::StructureData
• data_integrity_check() : core::sequence::SequenceAlignment
• 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_ptr() : core::conformation::Residue
• data_real() : protocols::denovo_design::components::StructureData
• data_real_ : protocols::denovo_design::components::StructureData
• data_source_ : protocols::toolbox::task_operations::ConservativeDesignOperation
• data_str() : protocols::denovo_design::components::StructureData
• data_str_ : protocols::denovo_design::components::StructureData
• data_struct() : core::scoring::data_struct
• database_ : core::scoring::hbonds::HBondEnergy
• database_dir() : protocols::farna::libraries::BasePairStepLibrary
• database_directory() : core::chemical::ResidueTypeSet
• database_directory_ : core::chemical::ResidueTypeSet
• 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
• DatabaseOccSolEne() : core::scoring::geometric_solvation::DatabaseOccSolEne
• 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 : core::pack::task::operation::TaskOperation , 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::SSElementMotifContactFilter , 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
• datamap_ : protocols::frag_picker::frag_movers::FragSetFromH5Mover
• DataPoint() : protocols::cluster::DataPoint
• dataset_ : protocols::toolbox::KClusterData
• datatype() : protocols::abinitio::abscript::JumpSampleData , protocols::environment::AutoCutData
• 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_dBdnmtr_ : core::scoring::FACTSResidueInfo
• dB_dBnmtr() : 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::rotamer_recovery::RRReporterSQLite , protocols::toolbox::task_operations::ReadResfileFromDB
• 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::annealer::FASTERAnnealer
• dBR_ : core::pack::interaction_graph::FASTERInteractionGraph
• dBR_dG() : core::scoring::FACTSResidueInfo
• dBR_dG_ : core::scoring::FACTSResidueInfo
• DbTrajectoryReader() : protocols::trajectory::DbTrajectoryReader
• DbTrajectoryRecorder() : protocols::canonical_sampling::DbTrajectoryRecorder
• DbTrajectoryWriter() : protocols::trajectory::DbTrajectoryWriter
• dbx : core::scoring::APBSResult
• dby : core::scoring::APBSResult
• dbz : core::scoring::APBSResult
• DC() : core::scoring::DC
• dc_from_pose() : core::scoring::methods::DipolarCouplingEnergy
• DC_lines : core::scoring::DipolarCoupling
• dc_score_ : core::scoring::methods::DipolarCouplingEnergy
• DC_TYPE : core::scoring::DC
• DC_TYPE_CC : core::scoring::DC
• DC_TYPE_CH : core::scoring::DC
• DC_TYPE_NC : core::scoring::DC
• DC_TYPE_NH : core::scoring::DC
• dcalibrate_ : protocols::noesy_assign::PeakAssignmentParameters , protocols::noesy_assign::StructureDependentPeakCalibrator
• dCCdB_fastRes() : core::scoring::electron_density::ElectronDensity
• dCCdBs() : core::scoring::electron_density::ElectronDensity
• dCCdx_aacen() : core::scoring::electron_density::ElectronDensity
• dCCdx_cen() : core::scoring::electron_density::ElectronDensity
• dCCdx_fastRes() : core::scoring::electron_density::ElectronDensity
• dCCdx_PointFast() : core::scoring::electron_density::ElectronDensity
• dCCdx_res() : core::scoring::electron_density::ElectronDensity
• 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
• DCcomputed() : core::scoring::DC
• dcenlist_from_pose() : core::scoring::CenRotEnvPairPotential , core::scoring::SmoothEnvPairPotential
• DCerr() : core::scoring::DC
• 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
• dchi4E_dchi4() : core::scoring::methods::ProClosureEnergy
• dchidevpen_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchidevpen_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchidevpen_dchi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchidevpen_dchi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchimean_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchimean_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchimean_domg() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchimean_domg_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchisd_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchisd_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchisd_domg() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dchisd_domg_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dCOM_ : protocols::constraints_additional::COMCoordinateConstraint
• Dconst() : core::scoring::DC , core::scoring::RDC
• 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_ : core::scoring::DC
• DCval_computed_ : core::scoring::DC
• 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
• DDP_lookup_table_ : core::scoring::ScoringManager
• DDPlookup() : core::scoring::interface_::DDPlookup
• DDPscore() : core::scoring::interface_::DDPscore
• dE_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_dev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_dev_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_dev_perchi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_dev_perchi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_rot() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_rot_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_semi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dbb_semi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_dev() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_dev_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_semi() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dE_dchi_semi_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• deallocate_array() : core::graph::ArrayPool< T >
• deallocate_arraypoolelement() : core::scoring::EnergyGraph
• 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_dump_icoor() : core::chemical::ResidueType
• 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_pause() : core::conformation::Conformation
• 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_residue_torsions() : core::conformation::Conformation
• 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
• DebuggingAnnealer() : core::pack::annealer::DebuggingAnnealer
• DebugOut_MpiFileBuffer() : protocols::jd2::DebugOut_MpiFileBuffer
• 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
• decide_cuts() : protocols::hybridization::HybridizeFoldtreeDynamic
• decide_if_sequence_recovery_improved() : protocols::optimize_weights::IterativeOptEDriver
• decide_is_d_aa() : core::io::NomenclatureManager
• decide_is_known_achiral() : core::io::NomenclatureManager
• decide_is_l_aa() : core::io::NomenclatureManager
• decide_procrastinate_hpatch_computations() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• decide_procrastinate_surface_computations() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• decide_read_from_binary() : core::pack::dunbrack::RotamerLibrary
• decide_read_from_binary_02() : core::pack::dunbrack::RotamerLibrary
• decide_read_from_binary_10() : core::pack::dunbrack::RotamerLibrary
• decide_to_keep_pose() : protocols::stepwise::monte_carlo::mover::DeleteMover
• decide_write_binary() : core::pack::dunbrack::RotamerLibrary
• decide_write_binary_02() : core::pack::dunbrack::RotamerLibrary
• decide_write_binary_10() : core::pack::dunbrack::RotamerLibrary
• declare_all_existing_rotwells_encountered() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• declare_all_rotamers_initialized() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• declare_atom_neighbor_1sided() : core::scoring::NeighborList
• declare_atoms_neighbors() : core::scoring::NeighborList
• declare_chemical_bond() : core::conformation::Conformation , core::conformation::symmetry::SymmetricConformation , protocols::environment::ProtectedConformation
• declare_covalent_bond() : protocols::denovo_design::components::StructureData
• declare_covalent_bond_in_pose() : protocols::denovo_design::components::StructureData
• declare_edge_energies_final() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• declare_energies_final() : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• declare_energies_final_no_deletion() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• declare_minimization_over() : protocols::optimize_weights::OptEMultifunc
• declare_polymer_bond() : protocols::denovo_design::components::StructureData
• declare_remodelable() : protocols::enzdes::EnzdesFlexibleRegion
• DeclareBond() : protocols::cyclic_peptide::DeclareBond
• decompose_bb_hb_into_pair_energies() : core::scoring::hbonds::HBondOptions
• decompose_bb_hb_into_pair_energies_ : core::scoring::hbonds::HBondOptions
• 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
• decoy_params_ : core::scoring::packing::HolesEnergy
• decoy_score : core::scoring::packing::HolesResult
• decoy_tag() : core::io::raw_data::RawStruct , core::io::silent::SilentStruct
• decoy_tag_ : core::io::raw_data::RawStruct , core::io::silent::SilentStruct
• DecoyFileData() : core::io::raw_data::DecoyFileData
• 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
• DecoyStruct() : core::io::raw_data::DecoyStruct
• decrease_double_lazy_ig_memlimit() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• decrease_linmem_ig_history_size() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• decreasing() : protocols::loops::Loop , protocols::nonlocal::Region
• decrement_from_cached() : core::pack::interaction_graph::RotamerDots
• decrement_reference_pose_mapping_after_seqpos() : core::pose::Pose , core::pose::reference_pose::ReferencePose , core::pose::reference_pose::ReferencePoseSet
• dEddofs_to_dEdvars() : protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• deep_clone() : core::scoring::constraints::Constraints
• deep_copy() : core::scoring::constraints::ConstraintSet
• deep_copy_from() : core::scoring::constraints::Constraints
• 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_ : 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 : core::scoring::PoissonBoltzmannPotential , protocols::pb_potential::SetupPoissonBoltzmannPotential
• default_bias_ : protocols::canonical_sampling::BiasEnergy
• default_build_hits_at_all_positions() : protocols::match::downstream::DownstreamAlgorithm
• default_commands() : core::pack::task::ResfileContents
• default_commands_ : core::pack::task::ResfileContents
• 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_filename() : core::pack::task::operation::ReadResfile
• 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_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() : core::chemical::ResidueLoader , core::conformation::symmetry::SymmDataLoader , core::import_pose::PoseFromPDBLoader , core::io::silent::SilentFileLoader , core::scoring::electron_density::ElectronDensityLoader , core::scoring::fiber_diffraction::FiberDiffractionLoader , protocols::loophash::LoopHashLibraryLoader , protocols::loops::LoopsFileLoader , protocols::surface_docking::SurfaceVectorLoader
• default_position : core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow
• default_position_from_affix() : core::chemical::carbohydrates::CarbohydrateInfoManager
• 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_rama_table_type() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• default_rama_table_type_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• default_repeating_unit_offset() : protocols::helical_bundle::MakeBundle
• default_repeating_unit_offset_ : protocols::helical_bundle::MakeBundle
• default_repeating_unit_offset_set() : 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_ : 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() : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , protocols::helical_bundle::PerturbBundleOptions
• 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_ : 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_bins() : protocols::magnesium::SampleGrid
• 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_residue_selector_xml_schema() : core::select::residue_selector::ResidueSelectorFactory
• define_start_window() : protocols::simple_moves::ClassicFragmentMover
• defined() : protocols::jumping::MembraneJump
• defined_adducts() : core::chemical::ResidueType
• defined_adducts_ : core::chemical::ResidueType
• 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_dof_derivatives() : core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::scoring::methods::carbohydrates::SugarBackboneEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::YHHPlanarityEnergy
• defines_high_order_terms() : core::scoring::constraints::ConstraintsEnergy , core::scoring::methods::EnergyMethod
• defines_intrares_dof_derivatives() : core::scoring::constraints::ConstraintsEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::rna::RNA_SuiteEnergy
• defines_intrares_energy() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::constraints::ConstraintsEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::TableLookupEtableEnergy , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody , core::scoring::hackaro::HackAroEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::interface_::DDPscore , core::scoring::lkball::LK_BallEnergy , core::scoring::magnesium::MgEnergy , core::scoring::magnesium::RNA_MgPointEnergy , core::scoring::membrane::FaMPSolvEnergy , core::scoring::membrane::MPPairEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_ReferenceEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::rna::data::RNA_DataBackboneEnergy , core::scoring::rna::RNA_FullAtomStackingEnergy , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_LJ_BaseEnergy , core::scoring::rna::RNA_PairwiseLowResolutionEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::rna::RNA_VDW_Energy , core::scoring::rna::StackElecEnergy , core::scoring::sym_e::symEnergy , core::scoring::vdwaals::VDW_Energy , protocols::scoring::methods::InterchainPairEnergy
• defines_intrares_energy_for_residue() : core::scoring::methods::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy
• defines_residue_pair_energy() : core::scoring::constraints::ConstraintsEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::GenBornEnergy , core::scoring::methods::LongRangeTwoBodyEnergy , core::scoring::methods::MultipoleElecEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::rna::RNA_JR_SuiteEnergy , core::scoring::rna::RNA_SuiteEnergy , core::scoring::rna::RNA_TorsionEnergy , core::scoring::sym_e::symEnergy
• defines_score_for_residue() : core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::OneBodyEnergy
• defines_score_for_residue_pair() : core::scoring::constraints::ConstraintsEnergy , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_GrpElecEnergy , core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator , core::scoring::geometric_solvation::OccludedHbondSolEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::rna::StackElecEnergy
• defines_score_for_rsd() : core::scoring::methods::YHHPlanarityEnergy
• 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
• degeneracy : core::chemical::rings::RingConformer
• degenerate_conformers_ : core::chemical::rings::RingConformerSet
• 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_act_coord_atom() : core::chemical::ResidueType
• delete_atom() : core::chemical::ResidueType , core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• delete_atom_alias() : core::chemical::ResidueType
• delete_chain_ending() : core::conformation::Conformation , protocols::environment::ProtectedConformation
• delete_checkpoints_ : protocols::checkpoint::CheckPointer
• delete_child_proton() : core::chemical::ResidueType
• 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_edge() : core::graph::Graph , core::graph::UEEdge< V, E > , core::kinematics::FoldTree , core::pack::interaction_graph::SimpleInteractionGraph , core::scoring::constraints::ConstraintGraph , core::scoring::EnergyGraph , core::scoring::MinimizationGraph , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborGraph , protocols::sewing::MonteCarloAssemblyMover , protocols::sewing::SewGraph
• delete_everything() : core::graph::Graph
• delete_extra_vertices() : core::kinematics::FoldTree
• delete_graph_edges_using_domain_map() : core::scoring::Energies
• delete_in_progress_files() : protocols::jd2::FileSystemJobDistributor
• delete_interface_native_sidechains() : protocols::anchored_design::AnchoredDesignMover
• delete_interface_native_sidechains_ : protocols::anchored_design::AnchoredDesignMover
• delete_jump_and_intervening_cutpoint() : core::kinematics::FoldTree , protocols::denovo_design::components::StructureData
• delete_jump_seqpos() : core::kinematics::FoldTree
• delete_leading_residues() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• delete_loop() : protocols::loops::Loops
• delete_metalbinding_atom() : core::chemical::ResidueType
• delete_mover_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• delete_polymer_residue() : core::conformation::Conformation , core::pose::Pose , protocols::environment::ProtectedConformation
• delete_pose() : protocols::features::ProteinSilentReport
• delete_pose_from_tag() : protocols::features::ProteinSilentReport
• delete_position() : core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile
• delete_probability_ : protocols::sewing::MonteCarloAssemblyMover
• delete_property() : core::chemical::ResidueType
• 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() : core::pose::PDBInfo
• delete_res_range_list_ : protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters
• delete_residue() : protocols::frags::FragLib , protocols::frags::TorsionFragmentLibrary
• delete_residue_range_slow() : core::conformation::Conformation , core::pose::Pose , protocols::environment::ProtectedConformation
• delete_residue_slow() : core::conformation::Conformation , core::pose::Pose , protocols::environment::ProtectedConformation
• delete_residues() : protocols::denovo_design::components::Segment
• delete_residues_in_pose() : protocols::denovo_design::components::StructureData
• delete_segment() : core::kinematics::FoldTree , protocols::denovo_design::components::StructureData
• delete_segment_nopose() : protocols::denovo_design::components::StructureData
• delete_segments() : protocols::sewing::Assembly
• delete_self_edges() : core::kinematics::FoldTree
• delete_seqpos() : core::kinematics::AtomTree , core::kinematics::FoldTree
• delete_seqpos_simple() : core::kinematics::FoldTree
• delete_source_residue() : core::id::SequenceMapping
• delete_submotif_info() : core::pose::full_model_info::FullModelInfo
• delete_target_residue() : core::id::SequenceMapping
• delete_terminal_chi() : core::chemical::ResidueType
• delete_trailing_residues() : protocols::denovo_design::components::Segment , protocols::denovo_design::components::StructureData
• delete_unordered_edge() : core::kinematics::FoldTree
• delete_virtual_residues_after_FastRelax_ : protocols::relax::FastRelax
• DeleteActCoordAtom() : core::chemical::DeleteActCoordAtom
• DeleteAtom() : core::chemical::DeleteAtom
• DeleteChainMover() : protocols::simple_moves::DeleteChainMover
• DeleteChainsMover() : protocols::simple_moves::DeleteChainsMover
• DeleteChildProton() : core::chemical::DeleteChildProton
• deleted() : core::graph::UEEdge< V, E >
• deleted_ : core::graph::UEEdge< V, E >
• DeleteMetalbindingAtom() : core::chemical::DeleteMetalbindingAtom
• DeleteMover() : protocols::stepwise::monte_carlo::mover::DeleteMover
• DeleteProperty() : core::chemical::DeleteProperty
• DeleteRegionMover() : protocols::grafting::simple_movers::DeleteRegionMover
• deletes_any_property() : core::chemical::ResidueTypeFinder
• deletes_any_variant() : core::chemical::ResidueTypeFinder
• deletes_atom() : core::chemical::DeleteAtom , core::chemical::PatchOperation
• deletes_atoms() : core::chemical::Patch , core::chemical::PatchCase
• deletes_properties() : core::chemical::Patch , core::chemical::PatchCase
• deletes_property() : core::chemical::DeleteProperty , core::chemical::PatchOperation
• deletes_variant() : core::chemical::DeleteVariantType , core::chemical::PatchOperation
• deletes_variants() : core::chemical::Patch , core::chemical::PatchCase
• DeleteTerminalChi() : core::chemical::DeleteTerminalChi
• DeleteVariantType() : core::chemical::DeleteVariantType
• delR_ : protocols::electron_density::DockIntoDensityMover
• delta() : core::pose::Pose , 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
• 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_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_components() : core::scoring::dna::DNATorsionPotential
• delta_components_ : core::scoring::dna::DNATorsionPotential
• delta_coms : protocols::simple_filters::SymmetricMotifFilter
• delta_cutoff() : core::chemical::rna::RNA_FittedTorsionInfo , core::pose::rna::RNA_SuiteName , core::scoring::dna::DNATorsionPotential
• 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_filter_thresholds_ : protocols::protein_interface_design::filters::FilterScanFilter
• delta_filters() : protocols::design_opt::GreedyOptMutationMover , 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_north() : core::chemical::rna::RNA_FittedTorsionInfo
• delta_north_potential_ : core::scoring::rna::RNA_TorsionPotential
• 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_guesses_ : protocols::helical_bundle::FitSimpleHelix
• 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_sasa_ : core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator
• delta_south() : core::chemical::rna::RNA_FittedTorsionInfo
• delta_south_potential_ : core::scoring::rna::RNA_TorsionPotential
• 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_guesses_ : protocols::helical_bundle::FitSimpleHelix
• 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
• 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 >
• 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 , protocols::farna::RNA_FragmentMonteCarlo
• dens_grad() : core::scoring::electron_density::ElectronDensity
• 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
• DenseEnergyContainer() : core::scoring::DenseEnergyContainer
• DenseIGRepacker() : protocols::pack_daemon::DenseIGRepacker
• DenseNeighborConstIterator() : core::scoring::DenseNeighborConstIterator
• DenseNeighborIterator() : core::scoring::DenseNeighborIterator
• DensePDEdge() : core::pack::interaction_graph::DensePDEdge
• DensePDInteractionGraph() : core::pack::interaction_graph::DensePDInteractionGraph
• DensePDInteractionGraphOP : protocols::pack_daemon::DenseIGRepacker
• DensePDNode() : core::pack::interaction_graph::DensePDNode
• density : core::scoring::electron_density::ElectronDensity , core::scoring::electron_density_atomwise::ElectronDensityAtomwise , core::scoring::sc::Atom , core::scoring::sc::MolecularSurfaceCalculator , protocols::hybridization::FragmentBiasAssigner , protocols::simple_moves::ThermodynamicData
• density_change_trigger() : core::scoring::electron_density::ElectronDensity
• density_grid_search() : protocols::electron_density::DockIntoDensityMover
• density_nbr() : protocols::hybridization::FragmentBiasAssigner
• density_redraw : protocols::viewer::GraphicsState
• density_sigma : protocols::viewer::GraphicsState
• densityPtr : protocols::viewer::triangleIterator
• DensityScoringClaimer() : protocols::topology_broker::DensityScoringClaimer
• dentropy_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• 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
• 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() : core::optimization::DOF_Node
• dependent_ : core::optimization::DOF_Node
• dependent_atoms() : core::conformation::symmetry::SymmetryInfo
• dependent_begin() : core::optimization::symmetry::SymMinimizerMap
• dependent_dof_names_ : protocols::optimize_weights::WrapperOptEMultifunc
• dependent_dof_nodes_ : core::optimization::symmetry::SymMinimizerMap
• dependent_dofs() : core::conformation::symmetry::SymmetryInfo
• dependent_end() : core::optimization::symmetry::SymMinimizerMap
• dependent_node_map_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• dependent_on() : protocols::forge::build::BuildInstruction
• dependent_residue_map_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• dependent_torsions() : core::conformation::symmetry::SymmetryInfo
• depends_on_polymer_lower() : core::chemical::AtomICoor
• depends_on_polymer_upper() : core::chemical::AtomICoor
• depends_on_residue_connection() : core::chemical::AtomICoor
• depermute() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• depermute_disulfide_list() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• deposition_date() : core::io::HeaderInformation
• deprecated_eval_atom_derivative() : core::scoring::constraints::ConstraintSet
• deprecated_eval_atom_derivative_for_residue_pairs() : core::scoring::constraints::ConstraintSet
• depth() : core::optimization::DOF_Node , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , protocols::frag_picker::VallResidue
• depth_ : core::optimization::DOF_Node , core::scoring::MembraneEmbed , core::scoring::MembraneTopology , protocols::viewer::triangle
• depth_first_connected_component_counting() : core::pack::interaction_graph::NodeBase
• deriv_ : core::scoring::rna::RNA_SuitePotential
• deriv_check() : core::optimization::MinimizerOptions , protocols::farna::options::RNA_MinimizerOptions , protocols::simple_moves::MinMover
• 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_local() : protocols::normalmode::NormalModeMinimizer
• deriv_check_result() : core::optimization::AtomTreeMinimizer , core::optimization::CartesianMinimizer , core::optimization::NumericalDerivCheckResult , protocols::normalmode::NormalModeMinimizer
• 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_to_stdout_ : core::optimization::MinimizerOptions
• deriv_check_verbose() : 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_multiply() : core::conformation::symmetry::SymmetryInfo
• deriv_phi_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• deriv_psi_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• deriv_score() : core::scoring::mm::MMLJEnergyTable , core::scoring::mm::MMLJScore
• deriv_type2name_ : core::scoring::hbonds::HBondTypeManager
• deriv_type_from_name() : core::scoring::hbonds::HBondTypeManager
• derivative_atom() : core::scoring::disulfides::DisulfideAtomIndices
• derivative_atom_types_ : core::scoring::disulfides::DisulfideAtomIndices
• derivative_graph() : core::scoring::symmetry::SymmetricEnergies
• derivative_graph_ : core::scoring::symmetry::SymmetricEnergies
• derivatives() : core::scoring::lkball::WaterBuilder
• DerivCheckDataPoint() : core::optimization::DerivCheckDataPoint
• derive_from_src_lib() : protocols::frags::TorsionFragmentLibrary
• derive_LW_orientation() : core::pose::rna::BasePair
• derive_peptide() : protocols::analysis::PeptideDeriverFilter
• derive_staple_constraints_() : protocols::simple_moves::PeptideStapleMover
• derived_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• derived_prepare_for_residue_pair() : core::scoring::etable::BaseEtableEnergy< Derived >
• DerivedSequenceMapping() : core::sequence::DerivedSequenceMapping
• derivs() : core::scoring::hbonds::HBond
• derivs_ : core::scoring::hbonds::HBond
• derivs_of_ray_distances_ : protocols::pockets::PlaidFingerprint
• DerivVectorPair : core::optimization::MinimizerMap , core::scoring::DerivVectorPair
• DescentDirectionAlgorithm() : core::optimization::DescentDirectionAlgorithm
• 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() : core::grid::CartGrid< T > , 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::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_all_aas_ : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_antigen() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_antigen_ : protocols::antibody::design::AntibodySeqDesignTFCreator , protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• design_any() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• design_cdrs_ : protocols::antibody::task_operations::RestrictToCDRsAndNeighbors
• 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_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
• 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_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_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_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_proline_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_protocol_ : protocols::antibody::design::AntibodyDesignMover
• design_protocol_enum_to_string() : protocols::antibody::design::AntibodyDesignEnumManager
• design_protocol_is_present() : protocols::antibody::design::AntibodyDesignEnumManager
• design_protocol_string_to_enum() : protocols::antibody::design::AntibodyDesignEnumManager
• design_protocol_to_enum_ : protocols::antibody::design::AntibodyDesignEnumManager
• design_protocol_to_string_ : protocols::antibody::design::AntibodyDesignEnumManager
• 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_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• design_shell() : protocols::toolbox::task_operations::DesignAroundOperation
• 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_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::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
• DesignContrast() : core::io::sequence_comparation::DesignContrast
• designed_residue() : protocols::dna::PDBOutput
• designed_residues_ : protocols::dna::PDBOutput
• DesignInfo : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• designing_ : core::pack::task::ResidueLevelTask_
• designing_residues() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• 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_result() : core::chemical::ResidueTypeSelectorSingle
• desired_result_ : core::chemical::ResidueTypeSelectorSingle
• desired_sequence_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup
• desired_ss_chars_ : protocols::match::SecondaryStructureMPM
• destroy() : boost::unordered_object_pool< T, UserAllocator >
• destruction_obs_hub_ : core::pose::Pose
• DestructionEvent : core::pose::Pose , core::pose::signals::DestructionEvent
• desymmeterize() : protocols::match::upstream::DunbrackSCSampler
• desymmeterize_ : protocols::match::upstream::DunbrackSCSampler
• desymmeterize_upstream_restype_for_constraint() : protocols::match::Matcher
• detach() : core::pose::datacache::ObserverCache , protocols::moves::PyMolObserver
• detach_after_modify() : protocols::forge::build::BuildInstruction
• detach_after_modify_ : protocols::forge::build::BuildInstruction
• detach_conformation_obs() : core::pose::Pose
• detach_connection_obs() : core::conformation::Conformation
• detach_destruction_obs() : core::pose::Pose
• detach_energy_obs() : core::pose::Pose
• detach_from() : core::pose::datacache::CacheableObserver , core::pose::metrics::PoseMetricContainer , core::pose::PDBInfo , protocols::boinc::BoincCurrentPoseObserver , protocols::forge::build::BuildInstruction , protocols::viewer::ConformationViewer , protocols::viewer::SilentObserver
• detach_from_conformation() : core::scoring::constraints::ConstraintSet
• detach_general_obs() : core::conformation::Conformation , core::pose::Pose
• detach_identity_obs() : core::conformation::Conformation
• detach_impl() : core::pose::datacache::CacheableObserver , core::pose::datacache::LengthEventCollector , core::pose::datacache::SpecialSegmentsObserver , protocols::moves::PyMolObserver , protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• detach_length_obs() : core::conformation::Conformation
• detach_topological_observer() : core::kinematics::AtomTree
• detach_xyz_obs() : core::conformation::Conformation
• detached_clone() : core::scoring::constraints::ConstraintSet , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet
• detached_copy() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , core::kinematics::AtomTree , core::pose::Pose , core::scoring::constraints::ConstraintSet , protocols::comparative_modeling::IgnoreSubsetConstraintSet , protocols::constraints_additional::MaxSeqSepConstraintSet
• detailed_balance() : protocols::canonical_sampling::CanonicalSamplingMover
• detailed_balance_ : protocols::canonical_sampling::CanonicalSamplingMover
• detailed_search() : protocols::hybridization::TMalign
• details : update_ResidueType_enum_files.EnumInfo
• 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_any_overlap_with_rotamer() : core::pack::interaction_graph::HPatchNode< V, E, G >
• detect_background_residue_and_first_class_residue_neighbors() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• detect_background_residue_and_first_class_residue_overlap() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• detect_bonds() : core::conformation::Conformation , protocols::simple_moves::DeleteChainsMover
• detect_bonds_ : protocols::simple_moves::DeleteChainsMover
• detect_camelid_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• detect_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• detect_connecting_subunits() : protocols::cryst::MakeLatticeMover , protocols::cryst::MakeLayerMover
• detect_design_interface_ : protocols::enzdes::DetectProteinLigandInterface
• detect_disulfides() : core::conformation::Conformation , core::conformation::symmetry::MirrorSymmetricConformation , core::conformation::symmetry::SymmetricConformation , protocols::denovo_design::components::StructureData
• detect_fullatom() : core::io::silent::SilentStruct
• detect_neighborship() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• detect_neighborship_with_node() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• detect_overlap() : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• detect_pseudobonds() : core::conformation::Conformation , protocols::simple_moves::DeleteChainsMover
• detect_pseudobonds_ : protocols::simple_moves::DeleteChainsMover
• 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_carbohydrate_polymer_info() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_check_Ctermini_for_this_chain() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_check_Ntermini_for_this_chain() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_correct_length() : protocols::features::LoopAnchorFeatures
• determine_crossover_behavior() : core::scoring::etable::BaseEtableEnergy< Derived >
• 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_if_designing() : core::pack::task::ResidueLevelTask_
• determine_if_repacking() : core::pack::task::ResidueLevelTask_
• determine_interface() : protocols::dna::DnaInterfaceFinder
• determine_IUPAC_names() : core::chemical::carbohydrates::CarbohydrateInfo
• determine_job_ids_to_run() : protocols::jd2::MPIWorkPartitionJobDistributor
• determine_job_list() : protocols::jd3::JobQueen
• determine_jobs_for_next_round() : protocols::jd3::JobDistributor
• 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_mg_orbital_frame() : protocols::magnesium::MgOrbitalFrameFinder
• determine_nonstandard_polymer_status() : core::conformation::Residue
• determine_overlap() : protocols::simple_moves::MergePDBMover , protocols::simple_moves::RepeatPropagationMover
• determine_polarization_groups() : core::scoring::MultipoleElecPotential
• determine_polymer_connections() : core::chemical::carbohydrates::CarbohydrateInfo
• 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_residue_connection() : core::scoring::etable::count_pair::CountPairFactory
• determine_rotcounts_for_restype() : core::pack::rotamer_set::ContinuousRotamerSet
• determine_same_chain_next() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_same_chain_prev() : core::io::pose_from_sfr::PoseFromSFRBuilder
• determine_score_variations() : protocols::jd2::archive::NormalizedEvaluatedArchive
• determine_separate_chemical_entity() : core::io::pose_from_sfr::PoseFromSFRBuilder
• 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
• dfade_max_ : core::scoring::hbonds::FadeInterval
• dfade_min_ : core::scoring::hbonds::FadeInterval
• DFIRE_Energy() : core::scoring::methods::dfire::DFIRE_Energy
• DFIRE_Potential() : core::scoring::methods::dfire::DFIRE_Potential
• dfpmin() : core::optimization::Minimizer
• dfpmin_armijo() : core::optimization::Minimizer
• DFPMinConvergedAbsolute() : core::optimization::DFPMinConvergedAbsolute
• DFPMinConvergedFractional() : core::optimization::DFPMinConvergedFractional
• dfs() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom
• dfs_cycle_finder() : protocols::sewing::RepeatAssemblyMover
• dfunc() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::func_1d , core::optimization::Multifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , core::scoring::CenHBPotential , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::DOF_Constraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::custom_pair_distance::DistanceFunc , core::scoring::disulfides::CaCbCb_Angle_Func , core::scoring::disulfides::CaCbCbCa_Dihedral_Func , core::scoring::disulfides::CB_Angle_Func , core::scoring::disulfides::Cb_Distance_Func , core::scoring::disulfides::CBSG_Dihedral_Func , core::scoring::disulfides::Cen_Distance_Func , core::scoring::disulfides::NCaCaC_Dihedral_Func , core::scoring::disulfides::SG_Dist_Func , core::scoring::disulfides::SGSG_Dihedral_Func , core::scoring::func::AmberPeriodicFunc , core::scoring::func::CharmmPeriodicFunc , core::scoring::func::CircularGeneral1D_Func , core::scoring::func::CircularHarmonicFunc , core::scoring::func::CircularPowerFunc , core::scoring::func::CircularSigmoidalFunc , core::scoring::func::CircularSplineFunc , core::scoring::func::ConstantFunc , core::scoring::func::CountViolFunc , core::scoring::func::EtableFunc , core::scoring::func::FadeFunc , core::scoring::func::FlatHarmonicFunc , core::scoring::func::Func , core::scoring::func::GaussianChainDoubleFunc , core::scoring::func::GaussianChainFunc , core::scoring::func::GaussianChainQuadrupleFunc , core::scoring::func::GaussianChainSingleFunc , core::scoring::func::GaussianChainTripleFunc , core::scoring::func::GaussianFunc , core::scoring::func::HarmonicFunc , core::scoring::func::IdentityFunc , core::scoring::func::KarplusFunc , core::scoring::func::LinearPenaltyFunction , core::scoring::func::MinMultiHarmonicFunc , core::scoring::func::MixtureFunc , core::scoring::func::PeriodicFunc , core::scoring::func::ScalarWeightedFunc , core::scoring::func::SigmoidFunc , core::scoring::func::SkipViolFunc , core::scoring::func::SoedingFunc , core::scoring::func::SOGFunc , core::scoring::func::SOGFunc_Impl , core::scoring::func::SplineFunc , core::scoring::func::SquareWell2Func , core::scoring::func::SquareWellFunc , core::scoring::func::SumFunc , core::scoring::func::TopOutFunc , core::scoring::func::USOGFunc , core::scoring::methods::LK_SigmoidalFunc , core::scoring::SmoothScoreTermCoeffs , protocols::electron_density::BfactorMultifunc , protocols::electron_density::VoxelSpacingMultifunc , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::jumping::ChainbreakDistFunc , protocols::ncbb::SecStructMinimizeMultiFunc , 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_component() : core::scoring::func::MixtureFunc
• 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_dCi() : core::scoring::FACTSResidueInfo
• dG_dCi_ : core::scoring::FACTSResidueInfo
• dG_dSASA_ratio : protocols::analysis::InterfaceData
• DGBindOptEData() : protocols::optimize_weights::DGBindOptEData
• 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
• Di_ : core::scoring::FACTSResidueInfo
• die() : core::scoring::etable::coulomb::Coulomb
• die_ : core::scoring::etable::coulomb::Coulomb
• diff_torsions : protocols::stepwise::modeler::rna::output_data_struct
• DiffAtomSasaFilter() : protocols::enzdes::DiffAtomSasaFilter
• difference_from() : core::chemical::gasteiger::GasteigerAtomTypeData
• difference_type : boost::unordered_object_pool< T, UserAllocator > , core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator , core::kinematics::RT , core::kinematics::tree::Atom , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• different_resgroup() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• different_restype() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• differentiate() : protocols::pack_daemon::ExpExpression , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::Mean , 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() : core::chemical::ResidueType , core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• dihedral_ : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• dihedral_atom_sets_ : core::chemical::ResidueType
• dihedral_between_bonded_children() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• dihedral_constraint_energy() : core::scoring::constraints::ConstraintEdge
• 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_rmsd() : protocols::frag_picker::DiversifyDihedralsSelector
• dihedral_sampling_data_ : core::scoring::carbohydrates::CHIEnergyFunction
• DihedralConstraint() : core::scoring::constraints::DihedralConstraint
• DihedralConstraintCreator() : core::scoring::constraints::DihedralConstraintCreator
• DihedralConstraintsScore() : protocols::frag_picker::scores::DihedralConstraintsScore
• dihedrallist : protocols::cartesian::MolecularDynamics
• DihedralPairConstraint() : core::scoring::constraints::DihedralPairConstraint
• DihedralPairConstraintCreator() : core::scoring::constraints::DihedralPairConstraintCreator
• dihedrals_ : protocols::ncbb::SecStructMinimizeMover
• dihedrals_for_atom() : core::chemical::ResidueType
• dihedrals_for_atom_ : core::chemical::ResidueType
• dijkstras() : protocols::toolbox::ResidueNetwork
• dim() : protocols::pockets::PocketGrid , protocols::toolbox::ClusterBase
• dim_ : protocols::pockets::PocketGrid , protocols::toolbox::ClusterBase
• dim_prods_ : protocols::match::OccupiedSpaceHash
• dime : core::scoring::APBSConfig
• dimension() : protocols::noesy_assign::CrossPeak
• dimension_etable_arrays() : core::scoring::etable::Etable
• dimension_memb_etable_arrays() : core::scoring::etable::MembEtable
• dimer1() : core::scoring::DimerPairing
• dimer1_ : core::scoring::DimerPairing
• dimer2() : core::scoring::DimerPairing
• dimer2_ : core::scoring::DimerPairing
• dimer_neighbor : core::scoring::Strands
• dimer_seqsep_cutoff_ : protocols::fldsgn::potentials::sspot::SSPairPotential
• DimerPairing() : core::scoring::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::base_pairs::BasePairStep
• DinucleotideStrandSequence : protocols::farna::libraries::BasePairStepSequence
• dip_score_ : core::scoring::methods::ResidualDipolarCouplingEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• DipolarCoupling : core::scoring::DC , core::scoring::DipolarCoupling
• DipolarCouplingEnergy() : core::scoring::methods::DipolarCouplingEnergy
• dipole() : core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleParameter
• dipole_ : core::scoring::MultipoleElecResidueInfo , core::scoring::MultipoleParameter
• dir() : protocols::jd2::archive::Batch
• dir_ : protocols::rigid::RigidBodyMover
• direction : protocols::hotspot_hashing::VectorPair
• direction_ : protocols::normalmode::NormalModeRelaxMover
• directory() : core::chemical::AtomTypeSet
• directory_ : core::chemical::AtomTypeSet , core::chemical::orbitals::OrbitalTypeSet , protocols::ligand_docking::WriteLigandMolFile
• DirectReadoutEnergy() : core::scoring::methods::DirectReadoutEnergy
• DirectReadoutPotential() : core::scoring::dna::DirectReadoutPotential
• dis() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• 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_ : 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_auto_update() : core::scoring::NeighborList
• 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_packing_and_design_ : protocols::antibody::task_operations::DisableAntibodyRegionOperation , protocols::antibody::task_operations::DisableCDRsOperation
• 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
• DisableAntibodyRegionOperation() : protocols::antibody::task_operations::DisableAntibodyRegionOperation
• DisableCDRsOperation() : protocols::antibody::task_operations::DisableCDRsOperation
• disabled_ : core::pack::task::ResidueLevelTask_ , protocols::checkpoint::CheckPointer , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• disallow_aas() : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , protocols::denovo_design::task_operations::ConsensusLoopDesignOperation
• disallow_bps_at_extra_min_res() : protocols::farna::options::RNA_FragmentMonteCarloOptions
• disallow_bps_at_extra_min_res_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• disallow_carboxyl_conjugation_at_glu_asp() : core::chemical::ResidueTypeFinder
• disallow_carboxyl_conjugation_at_glu_asp_ : core::chemical::ResidueTypeFinder
• disallow_current_slide() : protocols::simple_moves::symmetry::SymmetrySlider
• disallow_deletion_of_last_residue_ : protocols::stepwise::monte_carlo::mover::AddOrDeleteMover
• disallow_movement_of_input_res() : protocols::toolbox::AtomLevelDomainMap
• disallow_noncanonical_aas() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• disallow_pair() : protocols::denovo_design::connection::Connection
• disallow_properties() : core::chemical::ResidueTypeFinder
• disallow_properties_ : core::chemical::ResidueTypeFinder
• disallow_quench() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• disallow_quench_ : core::pack::annealer::SimAnnealerBase , core::pack::task::PackerTask_ , protocols::toolbox::task_operations::ModifyAnnealer
• disallow_realign() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• disallow_realign_ : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• disallow_resid() : core::pack::task::operation::OptH
• disallow_variants() : core::chemical::ResidueTypeFinder
• 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
• DisallowIfNonnative() : core::pack::task::operation::DisallowIfNonnative
• DisallowIfNonnativeRLT() : core::pack::task::operation::DisallowIfNonnativeRLT
• discard_conformation_domain_map() : core::scoring::Energies
• discard_jumps_ : protocols::topology_broker::FragmentJumpClaimer
• DISCONNECT : core::conformation::signals::ConnectionEvent
• disconnect_segments() : protocols::denovo_design::components::StructureData
• disconnected_segments() : protocols::sewing::Assembly
• DisembodiedAssembly() : protocols::sewing::DisembodiedAssembly
• disjoint_set_sizes() : core::graph::DisjointSets
• DisjointSets() : core::graph::DisjointSets
• 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
• dissimilarity_ : protocols::ncbb::SecStructFinder
• dist() : core::kinematics::ShortestPathInFoldTree , core::pose::rna::RNA_SuiteAssignment , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::LocalCoordinateConstraint , 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() : core::scoring::motif::ResPairMotif
• dist2_cut() : protocols::normalmode::NormalMode
• dist2_cut_ : protocols::normalmode::NormalMode
• dist_ : protocols::fldsgn::SheetConstraintGenerator , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::forge::constraints::NtoCConstraintGenerator
• dist_bb() : protocols::protein_interface_design::filters::RmsdSimpleFilter
• dist_cut2_ : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• dist_cutoff() : protocols::toolbox::CalcInterNeighborGroup , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• 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_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_midpoint_ : core::select::util::SelectResiduesByLayer
• dist_pair() : core::scoring::SecondaryStructurePotential
• dist_pow_ : core::pose::rna::RNA_SuiteName
• 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_tolerance_ : protocols::fldsgn::SheetConstraintGenerator
• 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() : core::chemical::Bond , core::chemical::orbitals::ICoorOrbitalData , core::chemical::orbitals::OrbitalType , core::fragment::picking_old::concepts::Extent< PageIterator > , core::fragment::picking_old::vall::scores::VallFragmentScore , core::kinematics::Jump , core::kinematics::RT , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::pack::dunbrack::cenrot::CentroidRotamerSampleData , core::scoring::saxs::DistanceHistogram , core::scoring::sc::_RESULTS , protocols::antibody::CDRDBPose , protocols::antibody::CDRDBSequence , 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_ : 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_4d() : core::pose::rna::RNA_SuiteName
• distance_7d() : core::pose::rna::RNA_SuiteName
• 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() : core::select::residue_selector::NumNeighborsSelector , protocols::features::ChargeChargeFeatures , protocols::features::SaltBridgeFeatures , protocols::matdes::InterfacePackingFilter
• 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 , protocols::toolbox::ClusterBase
• distance_matrix_ : protocols::contact_map::ContactMap
• distance_pair() : protocols::simple_moves::symmetry::SetupNCSMover
• distance_pair_ : protocols::simple_moves::symmetry::SetupNCSMover
• distance_range_ : protocols::sewing::NodeConstraint
• distance_record() : protocols::noesy_assign::FragsToAtomDist
• distance_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• distance_squared() : core::kinematics::RT , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::scoring::etable::AtomPairEnergy , protocols::frag_picker::VallResidue
• distance_squared_ : protocols::scoring::Interface
• distance_squared_cb() : protocols::frag_picker::VallResidue
• distance_squared_cen() : protocols::frag_picker::VallResidue
• distance_table_ : core::scoring::methods::GoapEnergy
• 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_to_closest_magnesium() : protocols::magnesium::MgScanner
• distance_weights_ : protocols::frag_picker::scores::ProfileScoreDistWeight
• DistanceBoundVector : protocols::noesy_assign::DistanceScoreMover
• DistanceChainbreakEnergy() : core::scoring::methods::DistanceChainbreakEnergy
• distanceFromStart : protocols::toolbox::Node
• DistanceFunc() : core::scoring::custom_pair_distance::DistanceFunc
• DistanceHistogram() : core::scoring::saxs::DistanceHistogram
• DistancePairConstraint() : core::scoring::constraints::DistancePairConstraint
• DistancePointToLine() : core::scoring::sc::MolecularSurfaceCalculator
• DistanceRecord() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• distances_ : core::chemical::RigidDistanceVisitor
• DistanceScoreMover() : protocols::noesy_assign::DistanceScoreMover
• DistanceSquared : protocols::flexpack::interaction_graph::OTFFlexbbNode
• distbin() : core::scoring::methods::GoapEnergy
• distbin_map() : core::scoring::methods::GoapEnergy
• 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_backbone_and_sidechain_ : core::pack::interaction_graph::OnTheFlyNode , core::pack::interaction_graph::SymmOnTheFlyNode
• distinguish_backbone_and_sidechain_for_node() : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• 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
• distribute_pseudo_base_atom_derivatives() : core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy
• 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
• disulf1_ : protocols::denovo_design::connection::ConnectTerminiWithDisulfide
• disulf2_ : protocols::denovo_design::connection::ConnectTerminiWithDisulfide
• disulf_atom_index() : core::scoring::disulfides::DisulfideAtomIndices
• 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_indices_ : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• disulfide_atom_name_ : core::chemical::ResidueType
• disulfide_bonded() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• 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_list() : protocols::protein_interface_design::movers::DisulfideMover
• disulfide_matching_potential_ : core::scoring::ScoringManager
• disulfide_params() : core::scoring::disulfides::CentroidDisulfidePotential
• 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_RT() : core::scoring::disulfides::DisulfideMatchingPotential
• disulfide_ss : protocols::forge::remodel::RemodelWorkingSet
• DisulfideAtomIndices() : core::scoring::disulfides::DisulfideAtomIndices
• DisulfideDistance() : protocols::frag_picker::scores::DisulfideDistance
• DisulfideEntropyFilter() : protocols::simple_filters::DisulfideEntropyFilter
• DisulfideFile() : core::io::raw_data::DisulfideFile
• 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
• DisulfideMatchingDatabase() : core::scoring::disulfides::DisulfideMatchingDatabase
• DisulfideMatchingEnergy() : core::scoring::disulfides::DisulfideMatchingEnergy
• DisulfideMatchingEnergyComponents() : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• DisulfideMatchingEnergyContainer() : core::scoring::disulfides::DisulfideMatchingEnergyContainer
• DisulfideMatchingNeighborConstIterator() : core::scoring::disulfides::DisulfideMatchingNeighborConstIterator
• DisulfideMatchingNeighborIterator() : core::scoring::disulfides::DisulfideMatchingNeighborIterator
• DisulfideMatchingPotential() : core::scoring::disulfides::DisulfideMatchingPotential
• DisulfideMover() : protocols::protein_interface_design::movers::DisulfideMover
• disulfides() : core::io::raw_data::DisulfideFile , protocols::simple_moves::ForceDisulfidesMover
• disulfides_ : core::io::raw_data::DisulfideFile , protocols::simple_moves::ForceDisulfidesMover
• disulfides_changed() : core::scoring::disulfides::CentroidDisulfideEnergyContainer , core::scoring::disulfides::DisulfideMatchingEnergyContainer , core::scoring::disulfides::FullatomDisulfideEnergyContainer
• DisulfidizeMover() : protocols::denovo_design::DisulfidizeMover
• DisulfJumpClaimer() : protocols::topology_broker::DisulfJumpClaimer
• disulfLandingRange : protocols::forge::remodel::RemodelData
• DisulfMinData() : core::scoring::disulfides::DisulfMinData
• disulfMobileRange : protocols::forge::remodel::RemodelData
• DisulfPairing() : protocols::jumping::DisulfPairing
• DisulfPairingLibrary() : protocols::jumping::DisulfPairingLibrary
• DisulfResNeighbConstIterator() : core::scoring::disulfides::DisulfResNeighbConstIterator
• DisulfResNeighbIterator() : core::scoring::disulfides::DisulfResNeighbIterator
• 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
• divides_backbone_and_sidechain_energetics() : core::scoring::carbon_hbonds::CarbonHBondEnergy , core::scoring::elec::FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy
• 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 >
• dk() : core::scoring::electron_density::OneGaussianScattering
• dK_dphi() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::CartBondedParameters
• dK_dpsi() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::CartBondedParameters
• 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
• dljatr_ : core::scoring::etable::Etable , core::scoring::etable::TableLookupEvaluator , core::scoring::rna::RNA_LJ_BaseEnergy
• dljrep() : core::scoring::etable::Etable
• dljrep_ : core::scoring::etable::Etable , core::scoring::etable::TableLookupEvaluator , core::scoring::rna::RNA_LJ_BaseEnergy
• dm() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• dmatrix_ : protocols::scoring::methods::saxs::PDDFEnergy
• DME_FilterMover() : protocols::simple_moves::DME_FilterMover
• 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_Potential
• DMS_values_ : core::scoring::rna::data::RNA_DMS_LowResolutionPotential , core::scoring::rna::data::RNA_DMS_Potential
• dmu_dphi() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::CartBondedParameters
• dmu_dpsi() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::CartBondedParameters
• dna_base_distance_constraints_ : core::scoring::dna::DNATorsionEnergy
• dna_base_positions_ : protocols::dna::DNAParameters
• DNA_base_potential_ : core::scoring::ScoringManager
• DNA_BaseEnergy() : core::scoring::methods::DNA_BaseEnergy
• DNA_BasePotential() : core::scoring::dna::DNA_BasePotential
• dna_chains() : protocols::dna::RestrictDesignToProteinDNAInterface
• dna_chains_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface
• dna_design_ : protocols::motifs::MotifDnaPacker
• dna_dihedral_potential_ : core::scoring::ScoringManager
• DNA_DihedralEnergy() : core::scoring::methods::DNA_DihedralEnergy
• DNA_DihedralPotential() : core::scoring::dna::DNA_DihedralPotential
• dna_dr_potential_ : core::scoring::ScoringManager
• dna_env_pair_potential_ : core::scoring::ScoringManager
• DNA_EnvPairEnergy() : core::scoring::methods::DNA_EnvPairEnergy
• DNA_EnvPairPotential() : core::scoring::dna::DNA_EnvPairPotential
• 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_ReferenceEnergy() : core::scoring::methods::DNA_ReferenceEnergy
• dna_seq_tag() : protocols::dna::DnaInterfacePacker
• 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
• DNABase() : protocols::dna::DNABase
• DNABasepair() : protocols::dna::DNABasepair
• DNABasestep() : protocols::dna::DNABasestep
• dnabform_ : core::scoring::ScoringManager
• DNABFormPotential() : core::scoring::dna::DNABFormPotential
• DnaChains() : protocols::dna::DnaChains
• DNAChiEnergy() : core::scoring::dna::DNAChiEnergy
• 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
• DNATorsionEnergy() : core::scoring::dna::DNATorsionEnergy
• DNATorsionPotential() : core::scoring::dna::DNATorsionPotential
• dneglnrotprob_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• dneglnrotprob_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dnmtr() : core::scoring::FACTSResidueInfo
• dnmtr_ : core::scoring::FACTSResidueInfo
• 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_apprx_ : core::scoring::FACTSPotential
• 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_classic_intrares() : core::scoring::etable::BaseEtableEnergy< Derived >
• do_classic_intrares_ : core::scoring::etable::BaseEtableEnergy< Derived >
• do_close_loops_ : protocols::farna::RNA_FragmentMonteCarlo
• do_clustering() : protocols::cluster::ClusterPhilStyle , protocols::stepwise::modeler::StepWiseMinimizer , protocols::toolbox::ClusterPhilStyle
• do_compute_jump_rmsd() : protocols::nonlocal::StarTreeBuilder
• do_correct_NH() : core::scoring::ResidualDipolarCoupling
• do_cter_insert_ : protocols::antibody::ModelCDRH3
• do_cyclic_permutation() : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• do_distributed_rerun() : protocols::abinitio::AbrelaxApplication
• do_dynamic_patching() : protocols::abinitio::IterativeBase
• do_fa_stack_scorefunction_checks() : core::scoring::methods::FreeDOF_Energy
• do_filter() : protocols::electron_density::DockIntoDensityMover
• 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_FragmentMonteCarlo
• do_redistribution() : protocols::cluster::ClusterPhilStyle
• do_refine_ : protocols::electron_density::DockIntoDensityMover
• do_refinement() : protocols::electron_density::DockIntoDensityMover
• do_remodel() : protocols::denovo_design::connection::Connection
• do_remodel_ : protocols::denovo_design::connection::Connection
• do_rerun() : protocols::abinitio::AbrelaxApplication
• do_restrict_absent_canonical_aas() : core::pack::task::ResidueLevelTask_
• do_rosetta_library_domain_check_ : protocols::farna::libraries::RNA_ChunkLibrary
• 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_score_dev() : core::scoring::methods::LinearChainbreakEnergy
• do_score_ovp() : core::scoring::methods::LinearChainbreakEnergy
• 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_stepwise_lores() : protocols::stepwise::modeler::StepWiseModeler
• 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
• DOA_orb_orb_splines_ : core::scoring::orbitals::OrbitalsLookup
• doAngleDerivatives() : protocols::cartesian::MolecularDynamics
• doBondDerivatives() : protocols::cartesian::MolecularDynamics
• 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_domain_map() : core::pose::full_model_info::FullModelInfo
• DOCK_ENS_CONF1 : core::pose::datacache::CacheableDataType
• DOCK_ENS_CONF2 : core::pose::datacache::CacheableDataType
• dock_high_res() : protocols::antibody::design::GeneralAntibodyModeler
• dock_into_dens_strategy_ : protocols::electron_density::SetupForDensityScoringMover
• dock_low_res() : protocols::antibody::design::GeneralAntibodyModeler
• 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_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
• 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::options::StepWiseMoveSelectorOptions
• 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_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::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
• 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
• DockingScoreFunction() : core::scoring::DockingScoreFunction
• DockingSlideIntoContact() : protocols::docking::DockingSlideIntoContact
• DockIntoDensityMover() : protocols::electron_density::DockIntoDensityMover
• DockLatticeMover() : protocols::cryst::DockLatticeMover
• 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
• does_overlap() : core::scoring::packstat::Circle
• dof() : core::conformation::Conformation , core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pack::scmin::ResidueAtomTreeCollection , core::pose::Pose , protocols::rigid::RigidBodyDofPerturbMover , protocols::sic_dock::CorrectionVisitor
• DOF3 : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• dof_ : protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofRandomizeMover , protocols::rigid::RigidBodyDofTransMover
• dof_access() : core::environment::DofPassport
• dof_change_propagates_to_younger_siblings_ : core::kinematics::tree::BondedAtom
• dof_changeset_ : core::kinematics::AtomTree
• dof_conformers_ : protocols::jumping::ResiduePairJump
• DOF_Constraint() : core::scoring::constraints::DOF_Constraint
• dof_constraints_ : core::scoring::constraints::ConstraintSet
• DOF_DataPoint() : core::optimization::DOF_DataPoint
• dof_deriv_1benmeths_ : core::scoring::MinimizationNode
• dof_deriv_1benmeths_begin() : core::scoring::MinimizationNode
• dof_deriv_1benmeths_end() : core::scoring::MinimizationNode
• dof_deriv_2benmeths_ : core::scoring::MinimizationNode
• dof_deriv_2benmeths_begin() : core::scoring::MinimizationNode
• dof_deriv_2benmeths_end() : core::scoring::MinimizationNode
• DoF_helix_index() : protocols::helical_bundle::BundleGridSamplerHelper
• DOF_ID : core::conformation::Conformation , core::conformation::symmetry::SymmetryInfo , core::id::DOF_ID
• dof_id() : core::id::DOF_ID_Range
• DOF_ID : core::kinematics::AtomTree , core::kinematics::MinimizerMapBase , core::kinematics::MoveMap , core::kinematics::tree::Atom
• dof_id() : core::optimization::DOF_DataPoint , core::optimization::DOF_Node
• DOF_ID : core::optimization::DOF_Node , core::optimization::MinimizerMap , core::pose::Pose , core::scoring::constraints::ConstraintSet
• dof_id() : core::scoring::constraints::DOF_Constraint
• 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_begin() : core::kinematics::MoveMap
• dof_id_end() : core::kinematics::MoveMap
• dof_id_from_torsion_id() : core::conformation::Conformation
• DOF_ID_Map() : core::id::DOF_ID_Map< T > , core::kinematics::MoveMap
• dof_id_map_ : core::kinematics::MoveMap
• DOF_ID_Mask : core::kinematics::AtomTree , core::kinematics::MoveMap , core::kinematics::tree::Atom
• DOF_ID_Range() : core::id::DOF_ID_Range
• 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_IDs : core::conformation::symmetry::SymmetryInfo
• 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_is_independent() : core::conformation::symmetry::SymmetryInfo
• dof_lower_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• DOF_Map : core::id::DOF_ID_Map< T >
• dof_map_ : core::id::DOF_ID_Map< T >
• dof_mask_ : core::pack::scmin::AtomTreeSCMinMinimizerMap
• dof_moved_ : core::conformation::Conformation
• DoF_name() : protocols::helical_bundle::BundleGridSamplerHelper
• DOF_Node() : core::optimization::DOF_Node
• dof_node() : core::pack::scmin::AtomTreeSCMinMinimizerMap
• DOF_Node : core::pack::scmin::AtomTreeSCMinMinimizerMap
• dof_node() : core::pack::scmin::CartSCMinMinimizerMap
• DOF_Node : core::pack::scmin::CartSCMinMinimizerMap
• dof_node() : core::pack::scmin::SCMinMinimizerMap
• dof_node_for_chi() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• dof_node_from_id() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• dof_node_pointer_ : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• DOF_NodeOP : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap
• DOF_Nodes : core::optimization::MinimizerMap
• dof_nodes() : core::optimization::MinimizerMap
• DOF_Nodes : core::optimization::symmetry::SymMinimizerMap
• dof_nodes() : 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_refold_index_ : core::kinematics::tree::Atom_
• dof_sample_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• DoF_sample_value() : 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_step_data_ : core::optimization::NumDerivCheckData
• DOF_TaskMap : protocols::simple_moves::MinMover
• dof_tasks_ : protocols::simple_moves::MinMover
• DOF_Type : core::kinematics::AtomTree , core::kinematics::MinimizerMapBase , core::kinematics::MoveMap , core::kinematics::tree::Atom , core::optimization::DOF_Node , core::optimization::MinimizerMap
• DoF_type() : protocols::helical_bundle::BundleGridSamplerHelper
• dof_type_begin() : core::kinematics::MoveMap
• dof_type_end() : core::kinematics::MoveMap
• dof_type_map_ : core::kinematics::MoveMap
• DOF_TypeMap : core::kinematics::MoveMap
• dof_upper_vals_ : protocols::helical_bundle::BundleGridSamplerHelper
• dof_val() : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• dof_val_ : core::optimization::DerivCheckDataPoint , core::optimization::DOF_DataPoint
• 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
• dofid_to_atoms_ : core::pack::scmin::CartSCMinMinimizerMap
• dofmover_compresses() : protocols::simple_moves::symmetry::SymmetrySlider
• dofname2jnum_ : core::conformation::symmetry::SymmetryInfo
• DofPassport() : core::environment::DofPassport
• DofPassportCOP : protocols::environment::ClientMover
• dofs() : protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::simple_moves::DOFHistogramRecorder
• 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_for_pose0_ : protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• dofs_info() : core::pose::copydofs::CopyDofsInfo
• dofs_info_ : core::pose::copydofs::CopyDofsInfo
• dofs_to_vars() : protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• DofUnlock() : protocols::environment::DofUnlock , protocols::environment::ProtectedConformation
• doKIC() : protocols::generalized_kinematic_closure::GeneralizedKIC
• domain_map() : core::kinematics::MinimizerMapBase , core::optimization::CartesianMinimizerMap , core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap , core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap , core::scoring::Energies , core::scoring::NeighborList , 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_map_during_minimization() : core::scoring::Energies
• domain_move_frequency_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• domain_parse_templates() : protocols::hybridization::HybridizeProtocol
• domain_visited_ : core::scoring::loop_graph::LoopGraph
• DomainAssembly() : protocols::abinitio::DomainAssembly , protocols::hybridization::DomainAssembly
• DomainInterfaceFilter() : protocols::simple_filters::DomainInterfaceFilter
• DomainMap : core::conformation::Conformation , core::scoring::Energies
• domains_all_templ_ : protocols::hybridization::HybridizeProtocol
• doMD() : protocols::cartesian::MolecularDynamics
• dominant() : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• dominant_ : core::conformation::ResidueKinWriter , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• dominant_suites : core::pose::rna::RNA_SuiteName
• doMinimising() : protocols::cartesian::MolecularDynamics
• don_bbg_in_bb_bb_hbond() : core::scoring::hbonds::HBondSet
• don_chem_type2name_ : core::scoring::hbonds::HBondTypeManager
• don_chem_type_from_name() : core::scoring::hbonds::HBondTypeManager
• don_deriv : core::scoring::hbonds::HBondDerivs
• don_dist_cutoff() : protocols::features::WaterFeatures
• don_dist_cutoff_ : protocols::features::WaterFeatures
• don_hatm() : core::scoring::hbonds::HBond
• don_hatm_ : core::scoring::hbonds::HBond
• don_hatm_is_backbone() : core::scoring::hbonds::HBond
• don_hatm_is_backbone_ : core::scoring::hbonds::HBond
• don_hatm_is_protein_backbone() : core::scoring::hbonds::HBond
• don_hatm_is_protein_backbone_ : core::scoring::hbonds::HBond
• don_res() : core::scoring::hbonds::HBond
• don_res_ : core::scoring::hbonds::HBond
• don_res_is_dna() : core::scoring::hbonds::HBond
• don_res_is_dna_ : core::scoring::hbonds::HBond
• don_res_is_protein() : core::scoring::hbonds::HBond
• don_res_is_protein_ : core::scoring::hbonds::HBond
• don_strength() : core::scoring::hbonds::HBondDatabase
• don_strength_lookup_ : core::scoring::hbonds::HBondDatabase
• don_type() : core::scoring::hbonds::HBEvalTuple
• 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
• donorRes_occludingRes_geometric_sol_intra() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• donorRes_occludingRes_geometric_sol_one_way() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• donorRes_occludingRes_geometric_sol_one_way_bb_bb() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• donorRes_occludingRes_geometric_sol_one_way_sc() : core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• 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
• dont_compute_cav_balls : core::scoring::packstat::SasaOptions
• dot() : core::scoring::EMapVector , core::scoring::EnergyEdge
• dot_coord() : core::pack::interaction_graph::RotamerDots
• dot_coords_ : core::pack::interaction_graph::RotamerDots
• dot_exposed() : core::pack::interaction_graph::InvRotamerDots
• 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
• DotSphere() : core::pack::interaction_graph::DotSphere
• double_lazy_ : protocols::toolbox::task_operations::SetIGTypeOperation
• double_lazy_ig() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• double_lazy_ig_ : core::pack::task::PackerTask_
• double_lazy_ig_memlimit() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• double_mutant_scan_ : protocols::pmut_scan::PointMutScanDriver
• DoubleDenseIGRepacker() : protocols::pack_daemon::DoubleDenseIGRepacker
• DoubleDensePDEdge() : core::pack::interaction_graph::DoubleDensePDEdge
• DoubleDensePDInteractionGraph() : core::pack::interaction_graph::DoubleDensePDInteractionGraph
• DoubleDensePDInteractionGraphOP : protocols::pack_daemon::DoubleDenseIGRepacker
• DoubleDensePDNode() : core::pack::interaction_graph::DoubleDensePDNode
• DoubleLayerKinematicAbinitio() : protocols::abinitio::DoubleLayerKinematicAbinitio
• DoubleLazyEdge() : core::pack::interaction_graph::DoubleLazyEdge
• DoubleLazyInteractionGraph() : core::pack::interaction_graph::DoubleLazyInteractionGraph
• DoubleLazyNode() : core::pack::interaction_graph::DoubleLazyNode
• down_jump_atom_ : protocols::simple_filters::JumpEvaluator
• down_stub_ : protocols::simple_filters::JumpEvaluator
• downcast_cstedge() : core::scoring::constraints::CstResNeighbConstIterator , core::scoring::constraints::CstResNeighbIterator
• downhill_accepts_ : protocols::moves::MoverStatistics
• DownJumpSRFD() : core::fragment::DownJumpSRFD
• downsample_pfront_poses() : protocols::design_opt::GreedyOptMutationMover
• downstream() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• downstream_algorithms() : protocols::match::Matcher
• downstream_algorithms_ : protocols::match::Matcher
• downstream_atom() : core::kinematics::Edge , core::kinematics::FoldTree
• 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_combine() : core::id::SequenceMapping
• 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_jump_residue() : core::kinematics::FoldTree
• downstream_jump_stub() : core::conformation::Conformation
• 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
• downstream_stub_atoms_ : core::fragment::DownJumpSRFD
• 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
• DP_Matrix() : core::sequence::DP_Matrix
• dphi : protocols::simple_moves::BBConRotMover , protocols::simple_moves::BBGaussianMover
• Dphi_ : core::scoring::func::KarplusFunc
• DPScoringScheme() : core::sequence::DPScoringScheme
• dr_cycles() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• dr_cycles_ : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• draw_random_phi_psi_from_cdf() : core::scoring::Ramachandran2B , core::scoring::Ramachandran
• draw_random_phi_psi_from_extra_cdf() : core::scoring::Ramachandran
• drawn_out_heavyatom_hydrogenatom_energy() : core::scoring::hbonds::HBondEnergy
• drdz : core::scoring::packstat::Circle
• drift() : protocols::simple_moves::GenericMonteCarloMover
• drift_ : protocols::protein_interface_design::movers::LoopOver , protocols::simple_moves::GenericMonteCarloMover
• drop_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• drop_all_edges() : core::graph::Graph , core::graph::Node , core::graph::UEVertex< V, E > , core::graph::UpperEdgeGraph< V, E > , core::pack::interaction_graph::NodeBase
• drop_all_edges_for_node() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• drop_background_edge() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::FirstClassNode< V, E, G >
• drop_edge() : core::graph::Graph , core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::NodeBase
• 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_rotamer() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• drop_rotamers() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• drop_rotamers_by_index() : core::pack::rotamer_set::RotamerSet , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• drop_rots_above_cutoff_ : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• drop_small_submatrices_where_possible() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::PDEdge
• drop_strand_pairs() : protocols::fldsgn::topology::StrandPairingSet
• drop_unsatisfied_voxels() : protocols::match::OccupiedSpaceHash
• drop_zero_submatrices_where_possible() : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T > , core::pack::interaction_graph::PDEdge
• drotprob_dbb() : core::pack::dunbrack::RotamerLibraryScratchSpace
• drotprob_dbb_ : core::pack::dunbrack::RotamerLibraryScratchSpace
• dry_run() : protocols::relax::RelaxProtocolBase
• dry_run_ : protocols::match::upstream::FullChiSampleSet , protocols::relax::RelaxProtocolBase
• ds_ : core::scoring::SecondaryStructurePotential
• ds_atom_ids_needed_ : protocols::match::downstream::TargetRotamerCoords
• ds_atom_present() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• ds_builders_ : protocols::match::output::DownstreamRMSEvaluator
• ds_find() : core::graph::DisjointSets
• 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
• ds_make_set() : core::graph::DisjointSets
• ds_union() : core::graph::DisjointSets
• dSA_dDi() : core::scoring::FACTSResidueInfo
• 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::output::PDBWriter
• dsbuilders_ : protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::output::PDBWriter , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::UpstreamDownstreamCollisionFilter
• dscore() : core::scoring::mm::MMBondAngleScore , core::scoring::mm::MMBondLengthScore , core::scoring::mm::MMTorsionScore
• 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_ca_dih_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_cbs_ds() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_cbs_ds_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_cs_ang() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_cs_ang_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_fa13() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_fa13_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_ss_dih() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_ss_dih_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_ss_dst() : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslf_ss_dst_ : core::scoring::disulfides::FullatomDisulfideEnergyComponents
• dslfc_ang() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_ang_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_bb_dih() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_bb_dih_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cb_dih() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cb_dih_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cb_dst() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cb_dst_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cen_dst() : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_cen_dst_ : core::scoring::disulfides::CentroidDisulfideEnergyComponents
• dslfc_rot() : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dslfc_rot_ : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dslfc_RT() : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dslfc_RT_ : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dslfc_trans() : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dslfc_trans_ : core::scoring::disulfides::DisulfideMatchingEnergyComponents
• dsolv() : core::scoring::etable::Etable
• dsolv1() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• 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
• 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
• 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
• dspos1_mode_ : protocols::match::output::BestMatchesCollection
• dspose_ : protocols::match::output::DownstreamRMSEvaluator
• dsq() : core::conformation::PointGraphEdgeData
• 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() : core::scoring::dssp::Dssp
• dssp() : core::scoring::dssp::Dssp , protocols::features::SecondaryStructureSegment , protocols::features::Segment
• Dssp : protocols::fldsgn::BluePrintBDR
• dssp : protocols::sewing::segment
• dssp1() : core::scoring::motif::ResPairMotif
• dssp2() : core::scoring::motif::ResPairMotif
• dssp_ : protocols::sewing::SewSegment
• dssp_codes_ : protocols::sewing::sampling::requirements::GlobalLengthRequirement
• dssp_featurizer() : core::scoring::dssp::Dssp
• 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_reduced() : core::scoring::dssp::Dssp
• dssp_reduced_IG_as_L() : core::scoring::dssp::Dssp
• dssp_reduced_IG_as_L_if_adjcent_H() : core::scoring::dssp::Dssp
• dssp_secstruct_ : core::scoring::dssp::Dssp
• dssp_state() : core::scoring::dssp::StrandPairingSet
• dssp_updated_ss : protocols::forge::remodel::RemodelData
• DsspDesignOperation() : protocols::toolbox::task_operations::DsspDesignOperation
• DsspMover() : protocols::moves::DsspMover
• 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_ : 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::relax::FastRelax
• dummy_ : core::scoring::dna::DNABFormPotential
• dummy_atomid_ : core::scoring::aa_composition_energy::SequenceConstraint
• dummy_cacheable_data_type : core::pose::datacache::CacheableDataType
• dummy_deriv : core::scoring::rna::RNA_LowResolutionPotential
• dummy_distance : core::scoring::GenBornPotential
• dummy_distance_ : core::scoring::FACTSPotential
• dummy_modify() : protocols::forge::build::BuildManager
• 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
• DummyClass() : protocols::toolbox::DummyClass
• dump() : core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::func_1d , core::optimization::Multifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , protocols::checkpoint::FileBuffer , protocols::electron_density::BfactorMultifunc , protocols::electron_density::VoxelSpacingMultifunc , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::ncbb::SecStructMinimizeMultiFunc , 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_aligned_motif() : core::scoring::motif::ResPairMotif
• dump_ASU() : protocols::simple_moves::PeriodicBoxMover
• dump_BRIX() : protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid
• dump_cif() : core::pose::Pose
• 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_every_ : protocols::simple_moves::PeriodicBoxMover
• dump_file() : core::pose::Pose , protocols::simple_filters::EvaluatedTrialMover
• dump_initial_results() : protocols::indel::IndelOptimizationMover
• dump_initial_results_ : protocols::indel::IndelOptimizationMover
• 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() : protocols::sewing::scoring::MotifScorer
• dump_motif_hit() : protocols::motifs::MotifHit
• dump_motifs_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dump_motifs_pdb() : core::scoring::motif::MotifHits
• 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() : core::pack::rotamer_set::RotamerSets , core::pose::Pose , core::scoring::motif::ResPairMotif , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::farna::options::RNA_BasicOptions , 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::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_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_resfile() : core::scoring::motif::MotifHits
• dump_rounds_ : protocols::mpi_refinement::MPI_Refine_Emperor
• dump_scored_pdb() : core::pose::Pose
• 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::matdes::MatDesGreedyOptMutationMover
• dump_table_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::simple_filters::NMerSVMEnergyFilter
• dump_threshold_ : protocols::ncbb::SecStructFinder
• dump_trisbpy() : protocols::sic_dock::scores::TrisBpyScore
• dump_vd_info() : core::chemical::ResidueType
• 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
• dun02() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• dun02_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::rotamers::SingleResiduePeptoidLibrary
• dun10 : core::init::pre_talaris_2013_behavior_settings
• dunbrack_accept() : protocols::simple_moves::sidechain_moves::SidechainMover
• DunbrackConstraint() : core::pack::dunbrack::DunbrackConstraint
• DunbrackConstraintCreator() : core::pack::dunbrack::DunbrackConstraintCreator
• DunbrackEnergy() : core::pack::dunbrack::DunbrackEnergy
• DunbrackRotamer() : core::pack::dunbrack::DunbrackRotamer< S, N, P >
• DunbrackRotamerLibrarySpecification() : core::chemical::rotamers::DunbrackRotamerLibrarySpecification
• DunbrackRotamerMeanSD() : core::pack::dunbrack::DunbrackRotamerMeanSD< S, N, P >
• DunbrackRotamerSampleData() : core::pack::dunbrack::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
• dvol : core::scoring::packing::SurfVolDeriv
• dw_dr() : core::scoring::elec::FAElecContextData
• 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
• dweight_ : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• dx : core::scoring::APBSResult , core::scoring::packstat::LR_AtomData , core::scoring::packstat::LR_MP_AtomData
• Dx2y2 : core::chemical::gasteiger::GasteigerAtomTypeData
• dx_filename_ : core::scoring::PoissonBoltzmannPotential
• Dxy : core::chemical::gasteiger::GasteigerAtomTypeData
• Dxz : core::chemical::gasteiger::GasteigerAtomTypeData
• dy : core::scoring::APBSResult , core::scoring::packstat::LR_AtomData , core::scoring::packstat::LR_MP_AtomData
• dynamic_grid_refinement() : protocols::match::MatcherTask
• dynamic_grid_refinement_ : protocols::match::Matcher , protocols::match::MatcherTask
• DynamicAggregateFunction() : protocols::pack_daemon::DynamicAggregateFunction
• Dyz : core::chemical::gasteiger::GasteigerAtomTypeData
• dz : core::scoring::APBSResult
• dz1_initial_ : protocols::helical_bundle::FitSimpleHelix
• Dz2 : core::chemical::gasteiger::GasteigerAtomTypeData