- d -

• d_phi() : protocols::frag_picker::PhiPsiTalosIO
• d_psi() : protocols::frag_picker::PhiPsiTalosIO
• daemon_set() : protocols::pack_daemon::MultistateFitnessFunction
• daemons() : protocols::pack_daemon::DaemonSet
• DaemonSet() : protocols::pack_daemon::DaemonSet
• DarcParticleSwarmMinimizer() : protocols::pockets::DarcParticleSwarmMinimizer
• DarcPSO_elsts_score_() : protocols::pockets::DarcParticleSwarmMinimizer
• DarcPSO_fp_compare_() : protocols::pockets::DarcParticleSwarmMinimizer
• data() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptEPositionData
• database_fname() : protocols::toolbox::task_operations::DatabaseThread
• database_table() : protocols::toolbox::task_operations::ReadResfileFromDB
• DatabaseEntryWorkUnit() : protocols::wum::DatabaseEntryWorkUnit
• DatabaseFilter() : protocols::features::DatabaseFilter
• DatabaseJobInputter() : protocols::features::DatabaseJobInputter
• DatabaseJobOutputter() : protocols::features::DatabaseJobOutputter
• DatabaseThread() : protocols::toolbox::task_operations::DatabaseThread
• DataBuffer() : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• DataLoader() : protocols::jd2::parser::DataLoader
• DataLoaderCreator() : protocols::jd2::parser::DataLoaderCreator
• DataLoaderFactory() : protocols::jd2::parser::DataLoaderFactory
• DataLoaderRegistrator() : protocols::jd2::parser::DataLoaderRegistrator< T >
• DataPoint() : protocols::cluster::DataPoint
• datatype() : protocols::abinitio::abscript::JumpSampleData , protocols::environment::AutoCutData
• db_session() : protocols::rotamer_recovery::RRReporterSQLite , protocols::toolbox::task_operations::ReadResfileFromDB
• DbTrajectoryReader() : protocols::canonical_sampling::DbTrajectoryReader , protocols::trajectory::DbTrajectoryReader
• DbTrajectoryRecorder() : protocols::canonical_sampling::DbTrajectoryRecorder
• DbTrajectoryWriter() : protocols::trajectory::DbTrajectoryWriter
• ddG() : protocols::ddg::ddGMover
• ddg() : protocols::seeded_abinitio::GrowPeptides
• ddG() : protocols::simple_moves::ddG
• ddg_based() : protocols::seeded_abinitio::SeedFoldTree
• ddG_for_single_residue() : protocols::simple_filters::AlaScan , protocols::simple_filters::DdGScan
• ddG_mover() : protocols::simple_filters::DdGScan
• ddG_threshold() : protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::simple_filters::RotamerBoltzmannWeight
• 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
• DdGScan() : protocols::simple_filters::DdGScan
• ddomain_pot() : protocols::hybridization::DDomainParse
• DDomainParse() : protocols::hybridization::DDomainParse
• deallocate_arrays() : protocols::sparta::Sparta::SpartaLib
• deallocate_buffers() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::ParallelTempering
• debug() : protocols::antibody::SnugDock , protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD , protocols::checkpoint::CheckPointer , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::toolbox::task_operations::SeqprofConsensusOperation
• debug_five() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_four() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_note_accepted_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_note_considered_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_note_projected_deltaE_of_considered_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_note_rejected_substitution() : protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
• debug_one() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_output() : protocols::ddg::ddGMover
• debug_print() : protocols::antibody::AntibodyNumberingParser
• debug_print_addresses() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• debug_print_hierarchy() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• debug_print_size_per_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• debug_three() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_two() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debug_zero() : protocols::loops::loop_mover::refine::SmallMinCCDTrial
• debugging_output() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• DebugOut_MpiFileBuffer() : protocols::jd2::DebugOut_MpiFileBuffer
• decide_cuts() : protocols::hybridization::HybridizeFoldtreeDynamic
• decide_if_sequence_recovery_improved() : protocols::optimize_weights::IterativeOptEDriver
• decide_to_keep_pose() : protocols::stepwise::monte_carlo::mover::DeleteMover
• declare_all_rotamers_initialized() : protocols::flexpack::interaction_graph::OTFFlexbbNode
• declare_chemical_bond() : protocols::environment::ProtectedConformation
• declare_energies_final() : protocols::flexpack::interaction_graph::MinimalistFlexbbEdge
• declare_minimization_over() : protocols::optimize_weights::OptEMultifunc
• declare_remodelable() : protocols::enzdes::EnzdesFlexibleRegion
• DeclareBond() : protocols::cyclic_peptide::DeclareBond
• decompose_structure() : protocols::medal::MedalMover , protocols::nonlocal::HelixRotate , protocols::nonlocal::SheetTranslate
• DecomposeAndReweightEnergiesCalculator() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• decoy_compatibility() : protocols::noesy_assign::PeakAssignment
• decoy_count() : protocols::boinc::Boinc
• decoys() : protocols::jd2::archive::ArchiveBase , protocols::wum::WorkUnit_SilentStructStore
• decoys_returned() : protocols::jd2::archive::Batch
• DecoySetEvaluation() : protocols::toolbox::DecoySetEvaluation
• decreasing() : protocols::loops::Loop , protocols::nonlocal::Region
• dEddofs_to_dEdvars() : protocols::normalmode::NormalModeMultifunc
• default_allow_bondangles() : protocols::helical_bundle::MakeBundle
• default_allow_bondangles_set() : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths() : protocols::helical_bundle::MakeBundle
• default_allow_bondlengths_set() : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals() : protocols::helical_bundle::MakeBundle
• default_allow_dihedrals_set() : protocols::helical_bundle::MakeBundle
• default_build_hits_at_all_positions() : protocols::match::downstream::DownstreamAlgorithm
• default_crick_params_file() : protocols::helical_bundle::MakeBundle
• default_crick_params_file_set() : protocols::helical_bundle::MakeBundle
• default_delta_omega0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_omega0_set() : protocols::helical_bundle::MakeBundle
• default_delta_omega1() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::PerturbBundle
• default_delta_omega1_all() : protocols::helical_bundle::MakeBundle
• default_delta_omega1_all_set() : protocols::helical_bundle::MakeBundle
• default_delta_t() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_delta_t_set() : protocols::helical_bundle::MakeBundle
• default_helix_length() : protocols::helical_bundle::MakeBundle
• default_helix_length_set() : protocols::helical_bundle::MakeBundle
• default_invert() : protocols::helical_bundle::MakeBundle
• default_invert_set() : protocols::helical_bundle::MakeBundle
• default_master() : protocols::match::output::WriteUpstreamHitKinemage
• default_omega0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_omega0_set() : protocols::helical_bundle::MakeBundle
• default_omega1() : protocols::helical_bundle::MakeBundle
• default_omega1_set() : protocols::helical_bundle::MakeBundle
• default_options() : protocols::loophash::LoopHashLibraryLoader , protocols::loops::LoopsFileLoader , protocols::membrane::io::LipoFileLoader , protocols::membrane::io::SpanFileLoader , protocols::surface_docking::SurfaceVectorLoader
• default_r0() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle
• default_r0_set() : protocols::helical_bundle::MakeBundle
• default_residue_name() : protocols::helical_bundle::MakeBundle
• default_residue_name_set() : protocols::helical_bundle::MakeBundle
• default_value() : protocols::helical_bundle::PerturbBundleOptions
• default_z1() : protocols::helical_bundle::MakeBundle
• default_z1_set() : protocols::helical_bundle::MakeBundle
• define_active_site_from_gridlig_file() : protocols::match::MatcherTask
• define_active_site_from_residue_radii_list() : protocols::match::MatcherTask
• define_loops() : protocols::docking::DockingHighResLegacy
• define_match_by_single_downstream_positioning() : protocols::match::MatcherTask
• define_moving_res() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• define_start_window() : protocols::simple_moves::ClassicFragmentMover
• defined() : protocols::jumping::MembraneJump
• defined_positions() : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• DefineMovableLoops() : protocols::seeded_abinitio::DefineMovableLoops
• defines_intrares_energy() : protocols::scoring::methods::InterchainPairEnergy
• defs2BuildPositions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• defs2BuildPositions_findts() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• degree() : protocols::sasa_scores::Poly
• delete_chain_ending() : protocols::environment::ProtectedConformation
• delete_content_only() : protocols::simple_filters::FileRemoveFilter
• delete_db() : protocols::loophash::LoopHashLibrary
• delete_diagonal_peaks() : protocols::noesy_assign::CrossPeakList
• delete_in_progress_files() : protocols::jd2::FileSystemJobDistributor
• delete_interface_native_sidechains() : protocols::anchored_design::AnchoredDesignMover
• delete_loop() : protocols::loops::Loops
• delete_polymer_residue() : protocols::environment::ProtectedConformation
• delete_pose() : protocols::features::ProteinSilentReport
• delete_pose_from_tag() : protocols::features::ProteinSilentReport
• delete_record() : protocols::features::FeaturesReporter , protocols::features::JobDataFeatures , protocols::features::PdbDataFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ProteinResidueConformationFeatures , protocols::features::ResidueConformationFeatures , protocols::features::ResidueFeatures , protocols::features::RotamerFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreTypeFeatures , protocols::features::StructureFeatures , protocols::features::StructureScoresFeatures , protocols::features::TrajectoryMapFeatures , protocols::features::UnrecognizedAtomFeatures
• delete_records_from_table() : protocols::features::FeaturesReporter
• delete_residue() : protocols::frags::FragLib , protocols::frags::TorsionFragmentLibrary
• delete_residue_range_slow() : protocols::environment::ProtectedConformation
• delete_residue_slow() : protocols::environment::ProtectedConformation
• DeleteMover() : protocols::stepwise::monte_carlo::mover::DeleteMover
• DeleteRegionMover() : protocols::grafting::simple_movers::DeleteRegionMover
• delta() : protocols::dna::DNABase , protocols::helical_bundle::PerturbBundleOptions , protocols::moves::IteratedConvergenceMover , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::movers::LoopLengthChange , protocols::simple_moves::ContingentAcceptMover
• 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_filters() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover , protocols::protein_interface_design::filters::FilterScanFilter
• delta_omega0() : 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::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• delta_omega1_all() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• 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_t() : protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::PerturbBundle
• 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_vect() : protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters
• deltaE_best() : protocols::enzdes::EnzdesFlexibleRegion
• DeltaFilter() : protocols::simple_filters::DeltaFilter
• deltaG_bind() : protocols::optimize_weights::DGBindOptEData
• DenseIGRepacker() : protocols::pack_daemon::DenseIGRepacker
• DensityMorphingMover() : protocols::electron_density::DensityMorphingMover
• DensityScoringClaimer() : protocols::topology_broker::DensityScoringClaimer
• 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
• dependent_on() : protocols::forge::build::BuildInstruction
• depth() : protocols::frag_picker::VallResidue
• deriv_check() : protocols::farna::RNA_Minimizer , protocols::simple_moves::MinMover
• deriv_check_local() : protocols::normalmode::NormalModeMinimizer
• deriv_check_result() : protocols::normalmode::NormalModeMinimizer
• derive_from_src_lib() : protocols::frags::TorsionFragmentLibrary
• derive_peptide() : protocols::analysis::PeptideDeriverFilter
• derive_staple_constraints_() : protocols::simple_moves::PeptideStapleMover
• derived_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• 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
• deserialize() : protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeAtom , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridManager , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::wum::DatabaseEntryWorkUnit , protocols::wum::WorkUnit_SilentStructStore , protocols::wum::WorkUnitBase
• design() : protocols::antibody::design::CDRGraftDesignOptions , protocols::antibody::design::CDRSeqDesignOptions , protocols::docking::DockingHighResLegacy , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::simple_moves::DesignRepackMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol
• design_all_aas() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_antigen() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_chain1() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_chain2() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• design_framework() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_layer() : protocols::flxbb::LayerDesignOperation
• design_loop() : protocols::toolbox::task_operations::RestrictToLoops
• design_mover() : protocols::simple_moves::MSDMover
• design_neighbors() : protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors
• design_only_target_residues() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• design_proline() : protocols::antibody::design::AntibodySeqDesignTFCreator
• design_refine() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• design_refine_cart_relax() : protocols::forge::remodel::RemodelMover
• design_refine_seq_relax() : protocols::forge::remodel::RemodelMover
• design_shell() : protocols::toolbox::task_operations::DesignAroundOperation
• design_strategy() : protocols::antibody::design::CDRSeqDesignOptions
• design_targets() : protocols::enzdes::EnzdesBaseProtocol
• design_targets_score() : protocols::enzdes::EnzdesBaseProtocol
• designable() : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::toolbox::task_operations::DatabaseThread
• designable_only() : protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter
• DesignableResiduesFilter() : protocols::protein_interface_design::filters::DesignableResiduesFilter
• DesignAroundOperation() : protocols::toolbox::task_operations::DesignAroundOperation
• designed_residue() : protocols::dna::PDBOutput
• DesignMinimizeHbonds() : protocols::protein_interface_design::movers::DesignMinimizeHbonds
• 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
• DesignVsNativeComparison() : protocols::enzdes::DesignVsNativeComparison
• desired_entity_history_size() : protocols::pack_daemon::TopEntitySet
• desired_loops() : protocols::LoopRebuild
• desired_remodelres_in_vicinity() : protocols::forge::remodel::ResidueVicinityInfo
• desymmeterize() : protocols::match::upstream::DunbrackSCSampler
• desymmeterize_upstream_restype_for_constraint() : protocols::match::Matcher
• detach() : protocols::moves::PyMolObserver
• detach_after_modify() : protocols::forge::build::BuildInstruction
• detach_from() : protocols::boinc::BoincCurrentPoseObserver , protocols::forge::build::BuildInstruction , protocols::viewer::ConformationViewer , protocols::viewer::SilentObserver
• detach_impl() : protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver
• detailed_balance() : protocols::canonical_sampling::CanonicalSamplingMover
• detailed_search() : protocols::hybridization::TMalign
• detect_and_set_camelid_CDR_H3_stem_type() : protocols::antibody::AntibodyInfo
• detect_and_set_regular_CDR_H3_stem_type() : protocols::antibody::AntibodyInfo
• detect_and_set_regular_CDR_H3_stem_type_new_rule() : protocols::antibody::AntibodyInfo
• detect_camelid_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• detect_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• detect_regular_CDR_H3_stem_type() : protocols::antibody_legacy::Antibody
• DetectProteinLigandInterface() : protocols::enzdes::DetectProteinLigandInterface
• DetectSymmetry() : protocols::simple_moves::symmetry::DetectSymmetry
• determine_all_match_relevant_downstream_atoms() : protocols::match::MatcherTask
• determine_atom_inds_for_restype() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• determine_best_constraint() : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• determine_correct_length() : protocols::features::LoopAnchorFeatures
• determine_cyclization_viability() : protocols::simple_moves::DisulfideInsertionMover
• determine_dna_interface() : protocols::dna::DnaInterfaceFinder
• determine_flexible_regions() : protocols::enzdes::EnzdesFlexBBProtocol
• determine_found_residues_compatibility() : protocols::enzdes::SecondaryMatchProtocol
• determine_interface() : protocols::dna::DnaInterfaceFinder
• determine_job_ids_to_run() : protocols::jd2::MPIWorkPartitionJobDistributor
• determine_largest_nbr_atom_distance() : protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO
• determine_loop() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• determine_loops_to_model() : protocols::forge::remodel::RemodelLoopMover
• determine_protein_interface() : protocols::dna::DnaInterfaceFinder
• determine_ramachandran_hash() : protocols::features::BetaTurnDetection
• determine_ramachandran_hash_for_residue_with_dihedrals() : protocols::features::BetaTurnDetection
• determine_redundant_conformer_groups() : protocols::match::downstream::LigandConformerBuilder
• determine_redundant_upstream_matchres() : protocols::match::output::OutputWriter
• determine_res_cb_deviation() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• determine_res_to_recompute() : protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator
• determine_score_variations() : protocols::jd2::archive::NormalizedEvaluatedArchive
• determine_target_downstream_res() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• determine_upstream_restypes() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList
• deviation() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• dfunc() : core::scoring::constraints::ChainbreakDistFunc , protocols::electron_density::BfactorMultifunc , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::normalmode::NormalModeMultifunc , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pockets::FingerprintMultifunc , protocols::pockets::PocketExemplarMultifunc , protocols::qsar::qsarOptFunc , protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd , protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1 , protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2 , protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3 , protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4
• dfunc_exact() : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• dfunc_numeric() : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• DGBindOptEData() : protocols::optimize_weights::DGBindOptEData
• DiffAtomSasaFilter() : protocols::enzdes::DiffAtomSasaFilter
• differentiate() : protocols::pack_daemon::ExpExpression , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::PowExpression , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VMax , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMin , protocols::pack_daemon::VMinBy
• diffuse_ring() : protocols::qsar::scoring_grid::SingleGrid
• dihedral_rmsd() : protocols::frag_picker::DiversifyDihedralsSelector
• DihedralConstraintsScore() : protocols::frag_picker::scores::DihedralConstraintsScore
• dijkstras() : protocols::toolbox::ResidueNetwork
• dim() : protocols::pockets::PocketGrid , protocols::toolbox::ClusterBase
• dimension() : protocols::noesy_assign::CrossPeak
• DimerPairing() : protocols::fldsgn::topology::DimerPairing
• dimsizes() : protocols::match::Bool3DGrid
• dir() : protocols::jd2::archive::Batch
• dis() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• dis_U1D1() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• dis_U1D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• disable() : protocols::ligand_docking::ResidueTorsionRestraints
• disable_autotemp() : protocols::simple_moves::rational_mc::RationalMonteCarlo
• disable_build_stage() : protocols::loop_modeling::LoopModeler
• disable_centroid_stage() : protocols::loop_modeling::LoopModeler
• disable_constraint_scoreterms() : protocols::enzdes::EnzdesBaseProtocol
• disable_design_for_non_designing_cdrs() : protocols::antibody::design::AntibodySeqDesignTFCreator
• disable_fullatom_stage() : protocols::loop_modeling::LoopModeler
• disable_ignorefinished() : protocols::jobdist::BaseJobDistributor
• disable_inprogress() : protocols::jobdist::BaseJobDistributor
• disable_output() : protocols::jobdist::BaseJobDistributor
• disable_proline_design() : protocols::antibody::design::AntibodySeqDesignTFCreator
• disable_sampling_of_loop_takeoff() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• disallow_current_slide() : protocols::simple_moves::symmetry::SymmetrySlider
• disallow_realign() : protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• display_constraint_residues() : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody_legacy::AntibodyModeler
• display_func() : protocols::viewer::ConformationViewer
• display_if_necessary() : protocols::viewer::ConformationViewer
• display_progress() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• dist() : protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::frag_picker::Contact , protocols::frag_picker::PhiPsiTalosIO , protocols::hybridization::TMalign , protocols::simple_filters::AlaScan , protocols::toolbox::ClusterBase
• dist2_cut() : protocols::normalmode::NormalMode
• dist_bb() : protocols::protein_interface_design::filters::RmsdSimpleFilter
• dist_cutoff() : protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator
• dist_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_track() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• distance() : protocols::antibody::clusters::CDRCluster , protocols::hybridization::DDomainParse , protocols::noesy_assign::CovalentCompliance , protocols::noesy_assign::FragsToAtomDist , protocols::scoring::Interface , protocols::scoring::InterfaceInfo , protocols::toolbox::task_operations::RestrictToInterface
• distance_bound() : protocols::noesy_assign::CrossPeak
• distance_cutoff() : protocols::features::ChargeChargeFeatures , protocols::features::SaltBridgeFeatures , protocols::matdes::InterfacePackingFilter
• distance_matrix() : protocols::toolbox::ClusterBase
• distance_pair() : protocols::simple_moves::symmetry::SetupNCSMover
• distance_record() : protocols::noesy_assign::FragsToAtomDist
• distance_squared() : protocols::frag_picker::VallResidue
• distance_squared_cb() : protocols::frag_picker::VallResidue
• distance_squared_cen() : protocols::frag_picker::VallResidue
• distance_threshold() : protocols::matdes::OligomericAverageDegreeFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::ResidueBurialFilter
• DistanceRecord() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• DistanceScoreMover() : protocols::noesy_assign::DistanceScoreMover
• distinguish_pucker() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• distribute_jobs_to_remote_daemons() : protocols::pack_daemon::DynamicAggregateFunctionDriver
• DistributionMap() : protocols::ligand_docking::DistributionMap
• disulfide_list() : protocols::protein_interface_design::movers::DisulfideMover
• DisulfideDistance() : protocols::frag_picker::scores::DisulfideDistance
• DisulfideEntropyFilter() : protocols::simple_filters::DisulfideEntropyFilter
• DisulfideFilter() : protocols::protein_interface_design::filters::DisulfideFilter
• DisulfideIdentity() : protocols::frag_picker::scores::DisulfideIdentity
• DisulfideInsertionMover() : protocols::simple_moves::DisulfideInsertionMover
• DisulfideMover() : protocols::protein_interface_design::movers::DisulfideMover
• disulfides() : protocols::simple_moves::ForceDisulfidesMover
• DisulfJumpClaimer() : protocols::topology_broker::DisulfJumpClaimer
• DisulfPairing() : protocols::jumping::DisulfPairing
• DisulfPairingLibrary() : protocols::jumping::DisulfPairingLibrary
• DisulfTemplate() : protocols::jumping::DisulfTemplate
• 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
• 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
• DME_FilterMover() : protocols::simple_moves::DME_FilterMover
• dna_chains() : protocols::dna::RestrictDesignToProteinDNAInterface
• dna_neighbors() : protocols::dna::DnaInterfaceFinder
• dna_positions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• dna_seq_tag() : protocols::dna::DnaInterfacePacker
• DNABase() : protocols::dna::DNABase
• DNABasepair() : protocols::dna::DNABasepair
• DNABasestep() : protocols::dna::DNABasestep
• DnaChains() : protocols::dna::DnaChains
• DnaDesignDef() : protocols::dna::DnaDesignDef
• DnaInterfaceFinder() : protocols::dna::DnaInterfaceFinder
• DnaInterfaceMinMover() : protocols::dna::DnaInterfaceMinMover
• DnaInterfaceMultiStateDesign() : protocols::dna::DnaInterfaceMultiStateDesign
• DnaInterfacePacker() : protocols::dna::DnaInterfacePacker
• DnaNeighbor() : protocols::dna::DnaNeighbor
• DNAParameters() : protocols::dna::DNAParameters
• DnaPosition() : protocols::dna::DnaPosition
• do_append() : protocols::stepwise::monte_carlo::mover::AddMover
• do_apply() : protocols::kinematic_closure::KicMover , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopModeler , protocols::loop_modeling::LoopMover , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::samplers::LegacyKicSampler , protocols::loop_modeling::utilities::AcceptanceCheck , protocols::loop_modeling::utilities::LoopFilter , protocols::loop_modeling::utilities::LoopMoverGroup , protocols::loop_modeling::utilities::PrepareForCentroid , protocols::loop_modeling::utilities::PrepareForFullatom
• do_caching() : protocols::frag_picker::scores::ABEGO_SS_Score , protocols::frag_picker::scores::AmbigCSScore , protocols::frag_picker::scores::AtomBasedConstraintsScore , protocols::frag_picker::scores::CachingScoringMethod , protocols::frag_picker::scores::CSScore , protocols::frag_picker::scores::DisulfideDistance , protocols::frag_picker::scores::FragmentCrmsd , protocols::frag_picker::scores::FragmentCrmsdResDepth , protocols::frag_picker::scores::FragmentDME , protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::scores::GunnCostScore , protocols::frag_picker::scores::HydrophobicityProfileSimilarity , protocols::frag_picker::scores::HydrophobicitySimilarity , protocols::frag_picker::scores::JCoupling , protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::MidPhiOut , protocols::frag_picker::scores::MidPsiOut , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::PCS_FragDistance , protocols::frag_picker::scores::Phi , protocols::frag_picker::scores::PhiPsiRmsd , protocols::frag_picker::scores::PhiPsiSquareWell , protocols::frag_picker::scores::ProfileScore , protocols::frag_picker::scores::ProfileScoreBlosum62 , protocols::frag_picker::scores::ProfileScoreDistWeight , protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::ProfileScoreSubMatrix , protocols::frag_picker::scores::Psi , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::RDCScore , protocols::frag_picker::scores::ScoreEValuator , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::SolventAccessibility , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::TorsionBinSimilarity
• do_caching_simple() : protocols::frag_picker::scores::ProfileScoreL1 , protocols::frag_picker::scores::ProfileScoreStructL1 , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• do_calibration() : protocols::noesy_assign::PeakCalibrator , protocols::noesy_assign::PeakCalibratorMap
• do_chain_closure_modeler() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• do_checks() : protocols::stepwise::modeler::align::StepWisePoseAligner
• do_checks_and_apply_protonated_H1_adenosine_variant() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup
• do_clustering() : protocols::cluster::ClusterPhilStyle , protocols::stepwise::modeler::StepWiseMinimizer , protocols::toolbox::ClusterPhilStyle
• do_compute_jump_rmsd() : protocols::nonlocal::StarTreeBuilder
• do_distributed_rerun() : protocols::abinitio::AbrelaxApplication
• do_dynamic_patching() : protocols::abinitio::IterativeBase
• do_final_repack() : protocols::relax::CentroidRelax
• do_frag_cycles() : protocols::loops::loop_closure::ccd::LoopClosure
• do_full_minimizing() : protocols::stepwise::modeler::StepWiseMinimizer
• do_init() : protocols::rpc::BasicCmdLineInit , protocols::rpc::BasicInit
• do_initialize() : protocols::md::CartesianMD
• 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_minimizing() : protocols::stepwise::modeler::StepWiseModeler
• do_not_sample_multiple_virtual_sugar() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• 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_random_fragment_insertions() : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• do_random_moves() : protocols::farna::RNA_DeNovoProtocol
• do_redistribution() : protocols::cluster::ClusterPhilStyle
• do_rerun() : protocols::abinitio::AbrelaxApplication
• do_rotation() : protocols::hybridization::TMalign
• do_same_strand() : protocols::jumping::SameStrand
• do_sampling() : protocols::stepwise::modeler::StepWiseModeler
• do_score() : protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::PNatLigPoseOptEData
• do_screen() : protocols::stepwise::screener::NativeRMSD_Screener
• do_some_clustering() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• do_some_filtering() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• do_stage1_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage2_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage3_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage3b_cycles() : protocols::abinitio::MembraneAbinitio
• do_stage4_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• do_stage5_cycles() : protocols::abinitio::ClassicAbinitio
• do_step() : protocols::abinitio::abscript::AbscriptMover::StageTracker
• do_strand_sum() : protocols::jumping::SameStrand
• do_sugar_sampling() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• do_superimposition() : protocols::stepwise::modeler::align::StepWisePoseAligner
• do_test_move() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• do_the_modeler() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• doAngleDerivatives() : protocols::cartesian::MolecularDynamics
• doBondDerivatives() : protocols::cartesian::MolecularDynamics
• dock_high_res() : protocols::antibody::design::AntibodyDesignModeler
• dock_low_res() : protocols::antibody::design::AntibodyDesignModeler
• dock_mcm_on_surface() : protocols::surface_docking::FullatomRelaxMover
• DockAndRetrieveSidechains() : protocols::protein_interface_design::movers::DockAndRetrieveSidechains
• DockDesignFilterFactory() : protocols::protein_interface_design::DockDesignFilterFactory
• docking() : protocols::antibody::SnugDockProtocol
• docking_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::monte_carlo::SWA_MoveSelector
• docking_highres_filter() : protocols::symmetric_docking::SymDockProtocol
• docking_highres_mover() : protocols::docking::DockingProtocol
• docking_jump() : protocols::topology_broker::AsymFoldandDockClaimer
• docking_lowres_filter() : protocols::symmetric_docking::SymDockProtocol
• docking_lowres_mover() : protocols::docking::DockingProtocol
• DockingEnsemble() : protocols::docking::DockingEnsemble
• DockingEnsemblePrepackProtocol() : protocols::docking::DockingEnsemblePrepackProtocol
• DockingHighRes() : protocols::docking::DockingHighRes
• DockingHighResFilter() : protocols::docking::DockingHighResFilter
• DockingHighResLegacy() : protocols::docking::DockingHighResLegacy
• DockingInitialPerturbation() : protocols::docking::DockingInitialPerturbation
• DockingLowRes() : protocols::docking::DockingLowRes
• DockingLowResEnsemble() : protocols::docking::DockingLowResEnsemble
• DockingLowResFilter() : protocols::docking::DockingLowResFilter
• DockingNoRepack1() : protocols::toolbox::task_operations::DockingNoRepack1
• DockingNoRepack2() : protocols::toolbox::task_operations::DockingNoRepack2
• DockingPrepackProtocol() : protocols::docking::DockingPrepackProtocol
• DockingProtocol() : protocols::docking::DockingProtocol
• DockingSlideIntoContact() : protocols::docking::DockingSlideIntoContact
• DockMCMCycle() : protocols::docking::DockMCMCycle
• DockMCMProtocol() : protocols::docking::DockMCMProtocol
• DockMinMover() : protocols::docking::DockMinMover
• DockSetupMover() : protocols::docking::DockSetupMover
• DockTaskFactory() : protocols::docking::DockTaskFactory
• DockWithHotspotMover() : protocols::protein_interface_design::movers::DockWithHotspotMover
• doDihedralDerivatives() : protocols::cartesian::MolecularDynamics
• does_final_fold_tree_exist() : protocols::topology_broker::TopologyBroker
• dof() : protocols::rigid::RigidBodyDofPerturbMover
• DoF_helix_index() : protocols::helical_bundle::BundleGridSamplerHelper
• dof_id_ranges() : protocols::backrub::BackrubMover , protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SmallMover
• DoF_name() : protocols::helical_bundle::BundleGridSamplerHelper
• DoF_sample_value() : protocols::helical_bundle::BundleGridSamplerHelper
• DoF_type() : protocols::helical_bundle::BundleGridSamplerHelper
• DofClaim() : protocols::topology_broker::claims::DofClaim
• DOFElement() : protocols::environment::claims::DOFElement
• DOFHistogramRecorder() : protocols::simple_moves::DOFHistogramRecorder
• dofmover_compresses() : protocols::simple_moves::symmetry::SymmetrySlider
• dofs() : protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::simple_moves::DOFHistogramRecorder
• dofs_for_pose0() : protocols::normalmode::NormalModeMultifunc
• dofs_to_vars() : protocols::normalmode::NormalModeMultifunc
• DofUnlock() : protocols::environment::DofUnlock
• doKIC() : protocols::generalized_kinematic_closure::GeneralizedKIC
• domain_assembly() : protocols::hybridization::HybridizeSetup
• domain_assembly_weights() : protocols::hybridization::HybridizeSetup
• DomainAssembly() : protocols::abinitio::DomainAssembly , protocols::hybridization::DomainAssembly
• DomainInterfaceFilter() : protocols::simple_filters::DomainInterfaceFilter
• doMD() : protocols::cartesian::MolecularDynamics
• dominant() : protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamHitKinemage
• doMinimising() : protocols::cartesian::MolecularDynamics
• don_dist_cutoff() : protocols::features::WaterFeatures
• 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
• DoubleDenseIGRepacker() : protocols::pack_daemon::DoubleDenseIGRepacker
• DoubleLayerKinematicAbinitio() : protocols::abinitio::DoubleLayerKinematicAbinitio
• downstream_algorithms() : protocols::match::Matcher
• downstream_atoms_required_inside_active_site() : protocols::match::MatcherTask
• downstream_builder() : protocols::match::Matcher
• downstream_builders() : protocols::match::Matcher
• downstream_conf_id() : protocols::match::downstream_hit , protocols::match::Hit
• downstream_hit() : protocols::match::downstream_hit
• downstream_orientation_atoms() : protocols::match::MatcherTask
• downstream_pose() : protocols::match::Matcher , protocols::match::MatcherTask
• downstream_pose_from_hit() : protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder
• downstream_res() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• downstream_res_nr() : protocols::jumping::JumpSample
• DownstreamAlgorithm() : protocols::match::downstream::DownstreamAlgorithm
• DownstreamBuilder() : protocols::match::downstream::DownstreamBuilder
• DownstreamCoordinateKinemageWriter() : protocols::match::output::DownstreamCoordinateKinemageWriter
• DownstreamRMSEvaluator() : protocols::match::output::DownstreamRMSEvaluator
• dp() : protocols::fldsgn::topology::DimerPairing
• DP_iter() : protocols::hybridization::TMalign
• dr_cycles() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• drift() : protocols::simple_moves::GenericMonteCarloMover
• drop_inter_group_edges() : protocols::simple_moves::GreenPacker
• drop_intra_group_edges() : protocols::simple_moves::GreenPacker
• drop_random_rate() : protocols::topology_broker::ConstraintClaimer
• drop_strand_pairs() : protocols::fldsgn::topology::StrandPairingSet
• drop_unsatisfied_voxels() : protocols::match::OccupiedSpaceHash
• dry_run() : protocols::relax::RelaxProtocolBase
• ds_atom_present() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• ds_hitset_end_its() : protocols::match::output::CloudPDBWriter
• ds_hitset_its() : protocols::match::output::CloudPDBWriter
• dsbuilders() : protocols::match::output::PDBWriter
• dspos1_mode() : protocols::match::output::BestMatchesCollection
• dssp_phi() : protocols::frag_picker::VallResidue
• dssp_psi() : protocols::frag_picker::VallResidue
• DsspDesignOperation() : protocols::toolbox::task_operations::DsspDesignOperation
• DsspMover() : protocols::moves::DsspMover
• dt() : protocols::md::MDBase
• dtest_cutoff() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• DualMonteCarlo() : protocols::moves::DualMonteCarlo
• dualspace() : protocols::relax::FastRelax
• dummy_modify() : protocols::forge::build::BuildManager
• DummyClass() : protocols::toolbox::DummyClass
• dump() : protocols::checkpoint::FileBuffer , protocols::electron_density::BfactorMultifunc , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::normalmode::NormalModeMultifunc , protocols::pockets::FingerprintMultifunc , protocols::pockets::PocketExemplarMultifunc , protocols::qsar::qsarOptFunc , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions
• dump_BRIX() : protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid
• dump_conformer() : protocols::ligand_docking::Transform
• dump_debug_pdb() : protocols::scoring::ImplicitFastClashCheck
• dump_decoy_or_score() : protocols::canonical_sampling::CanonicalSamplingMover
• dump_eggshell() : protocols::pockets::EggshellGrid
• dump_file() : protocols::simple_filters::EvaluatedTrialMover
• dump_invrots_tree_as_multimodel_pdbs() : protocols::toolbox::match_enzdes_util::InvrotTree
• dump_jump_log() : protocols::abinitio::KinematicAbinitio
• dump_linkers() : protocols::sic_dock::LinkerScore
• dump_matching_motifs() : protocols::sic_dock::scores::MotifHashRigidScore
• dump_minimal_pdb() : protocols::sic_dock::Rose
• dump_motif_hit() : protocols::motifs::MotifHit
• dump_oriented_pose_and_fp_to_pdb() : protocols::pockets::PlaidFingerprint
• dump_packertask() : protocols::flxbb::DesignTask
• dump_PCS_info() : protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• dump_pdb() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::protein_interface_design::filters::FilterScanFilter , protocols::sic_dock::Rose
• dump_pdb_to_file() : protocols::helix_capper::HelixNCapperMover , protocols::vip::VIP_Mover
• dump_pdb_when_fail() : protocols::fldsgn::BluePrintBDR
• dump_pdbs() : protocols::ddg::ddGMover , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• dump_pose() : protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::PDBJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor
• dump_pose_and_map() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor
• dump_pose_fname() : protocols::simple_filters::RelativePoseFilter
• dump_poses() : protocols::md::CartesianMD
• dump_pymol() : protocols::jumping::JumpSample
• dump_scores() : protocols::jobdist::PlainPdbJobDistributor
• dump_scoring_table() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• dump_silent() : protocols::jobdist::PlainSilentFileJobDistributor
• dump_structures() : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement , protocols::mpi_refinement::Serial_Refine
• dump_table() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• dump_trisbpy() : protocols::sic_dock::scores::TrisBpyScore
• dump_weights() : protocols::noesy_assign::PeakAssignment
• dump_xtc_format_decoy() : protocols::canonical_sampling::CanonicalSamplingMover
• dumpExemplarToFile() : protocols::pockets::PocketGrid
• dumpGridToFile() : protocols::pockets::PocketGrid
• DumpPdb() : protocols::simple_moves::DumpPdb
• dumpTargetPocketsToFile() : protocols::pockets::PocketGrid
• dumpTargetPocketsToPDB() : protocols::pockets::PocketGrid , protocols::pockets::TargetPocketGrid
• dunbrack_accept() : protocols::simple_moves::sidechain_moves::SidechainMover
• DunbrackSCSampler() : protocols::match::upstream::DunbrackSCSampler
• duplicate_residues_by_type() : protocols::simple_moves::RepeatPropagationMover
• dynamic_grid_refinement() : protocols::match::MatcherTask
• DynamicAggregateFunction() : protocols::pack_daemon::DynamicAggregateFunction